I am creating a Artificer and picked the Infusion for Homunculus Servant.

I added it in my Equipment, picked a gem, and it added the Homunculus Servant to my Extra tab.

The Skills, Saves, and Attack info are not showing correctly based on my characters Proficiency Bonus.

Homunculus Servant Stats

The Perception and Stealth should be +6, the Dex Save should be +6, the attack bonus should be +6, and the damage bonus should be +4.
For some reason the Perception is showing as +2, which make no sense since the base stat block under the Monster area shows it as +4.
I have tried clearing my cache, using a different browser and PC and get the same thing.

I also have an issue with mine. It looks like the Homunculus Servant might be using my Intelligence modifier (+2) in in place of my Proficiency Bonus (+3) when calculating all of these stats.

I have the same problem. Any fix except from maybe creating a new monster and using it?

I believe the Homunculus falls under this note from the OP of the Tasha's Support thread:

Scaling Statblocks

Several of the new features and spells present Monster Statblocks which scale with your character. This includes spells that summon other creatures. The system to handle these creatures is still under development but we have included inline stat blocks wherever possible to help you reference the stats you need.

This means, I believe, that the Homunculus you currently see under extras was likely part of the UA and/or Eberron's earlier version of the Artificer and has been left there for players using those versions of the artificer.  Until they can get a system going for these kinds of statblocks, yes, you will need to homebrew your own.  You can start by making a copy of the current statblock and make changes from there: I think that should save you some time.  

Yes, you can homebrew it, but you will have one minor thing you won’t be able to get quite correct. Either the Saving Throws will be too low, or the CR will be too high. The proficiency bonus is based on CR, so if you make the CR correct it will give the Setvant a lower Proficiency bonus than yours, so the Saves will be low. And if you bump their CR high enough to get the Saves correct, then it will display the Servants PB as way too high for anything else you might need to use it to calculate on the fly.

I have noticed this exact problem as a multi-classed Artificer with only 2 levels of Artificer.    At first I thought it was somehow only counting my PB from my two levels in Artificer (which is =2 at level 2), but I knew that didn't make sense because nothing else in DnD works that way.  I decided to check it out anyway, and no luck.    I made a level 20 artificer and the PB=2 value was still there in the statblock.   So I started playing around with Ability Scores.  The PB value is also definitely not referencing ability scores - I played with all of them.  It is also not referencing initiative.   Then I thought, "Well maybe they somehow linked it to my selection of it as a Level 2 Infusion."   So I went and shuffled my infusion selections to change it to a level 18 infusion, and the PB still didn't change.   I can't for the life of me affect that PB=2 value that is populating that statblock.  It's hard written in somewhere as far as I can tell.  

The PB is determined by the creature’s CR. They haven’t figured out how to have it draw from the Character’s PB yet.

I have found you can add a minus figure to the bonus side when you edit the proficiencies. So if its not looking right and higher than it should, put the number it should be for its main bonus, then minus for the extra, adjust the main till you can get it right.

So, any word on this issue? It looks like its still off for my new character. 

Once it is fixed/addressed, that fact should be noted on the second post of the Tasha’s support thread I linked to above.  Aside from that, we are not likely to get updates here about it’s status.  

How does the servants stats scale then? Can anyone break down how as I’m not getting my head around it.

It seems it’d be easier if it was just add PB or spell attack. 

If i understand coorectly, you simply add your PB to the modifier on the specified skills and saves. If I read the statblock correctly it shows skills with the servants modifier plus your PB of +2 at level 1. Only thing Im confused about is why perception is the same as stealth

The statblock is inaccurate.

Still not working properly. 

I think they've just decided to never fix it. 
I'd be fine with having a drag down menu in the statblock to input the artificer level, prof bonus, and intelligence and have it calculate the appropriate stats from there. Ideally, it would just automatically detect those things, but being able to select those 3 things and then have it do simple math to present the right stats would be a huge improvement.
Tasha's was released in late 2020. It's now April 2022 and... no fixes to these PB scaling things, like the homunculus servant and most of the summons from Tasha's.
Artificer in general is pretty badly implemented on DNDbeyond, they've never gotten a good way to manage infusions elegantly, and it doesn't know how to handle the armorer's extra infusions or being able to infuse the armor's weapons after level 9.
It's either really difficult to implement and/or they just don't feel any pressure to fix it because it's not hurting them enough opinion wise. Disappointing, to be sure.

I wish I could at least manually edit it. This and infusions are still broken in various ways and seemingly never addressed.

Gotta say it's pretty outrageous that this is still not fixed. The product has been out for over 18 months now. What's going on DDB? 

Could this please be addressed? Surely one of the dozens of bugs with this website could've been handled in the time span since the last update on Tasha's material, which was Feb 12, 2020.

I can't seriously recommend the character builder until WoTC cleans up some of the mess, there's just too many issues that a pen and paper character sheet doesn't have.

One tip for workaround:

1., I created a homebrew "monster". I picked the Tiny Servant and modified it. My PC is a lvl4 artificer + lvl1 wizard, my homonculus servant is here:

https://www.dndbeyond.com/monsters/2736166-zmeyavich-stravinsky-zmeya

2., You have to work the CR setting to correcly setup the Homonculus Servant's Proficiency Bonus. In my case I had to set the CR to 5 to reach PB 3.

3., Manually set the Ability Scores, HP, skills, etc.

4. After you finished your monster, you can go to your charater sheet. At the "Extras" section, click to "Manage Extras", choose "Misc" category and type in the name of your monster. Voila, you can see your Homonculus Servant with the correct stats.

5., You have to manually modify your monter's stats when you gain an Artificer level or your PB is increase.

6., If you want clickable stats, you can create an encounter, your PC against the HS. You can click on attack, saving throws, etc. in the encounter.

Quote from Rwombat >>

I think they've just decided to never fix it. 
I'd be fine with having a drag down menu in the statblock to input the artificer level, prof bonus, and intelligence and have it calculate the appropriate stats from there. Ideally, it would just automatically detect those things, but being able to select those 3 things and then have it do simple math to present the right stats would be a huge improvement.
Tasha's was released in late 2020. It's now April 2022 and... no fixes to these PB scaling things, like the homunculus servant and most of the summons from Tasha's.
Artificer in general is pretty badly implemented on DNDbeyond, they've never gotten a good way to manage infusions elegantly, and it doesn't know how to handle the armorer's extra infusions or being able to infuse the armor's weapons after level 9.
It's either really difficult to implement and/or they just don't feel any pressure to fix it because it's not hurting them enough opinion wise. Disappointing, to be sure.

 Ditto. All of this is still an issue and it doesn't seem likely to get fixed any time soon.