I have a Lvl. 7 Rogue Arcane Trickster with the Charlatan background- 16 Int, 18 Dex. Rogue gives you proficiency in Thieves Tools plus 4 skills of your choice, and Charlatan background gives you proficiency in 2 skills for a total of 6 + Thieves Tools. 
So I took my proficiencies in:

Arcana
Acrobatics
Investigation
Deception
Stealth
Slight of Hand

As a 7 Lvl. Rogue I gain Expertise in 4 skills, which doubles my proficiency. I took:

Investigation 

Deception

Stealth

Slight of Hand

However,  D&D Beyond will not add either my Proficiency or Expertise to my Investigation skill, only showing my Intelligence modifier of +3 on the Skills list. I have had to manually customize it as I have found no other way to correct it. Can someone please explain this to me as it seems like a system bug. 

Quote from KathydrBing >>

I have a Lvl. 7 Rogue Arcane Trickster with the Charlatan background- 16 Int, 18 Dex. Rogue gives you proficiency in Thieves Tools plus 4 skills of your choice, and Charlatan background gives you proficiency in 2 skills for a total of 6 + Thieves Tools. 
So I took my proficiencies in:

Arcana
Acrobatics
Investigation
Deception
Stealth
Slight of Hand

As a 7 Lvl. Rogue I gain Expertise in 4 skills, which doubles my proficiency. I took:

Investigation 

Deception

Stealth

Slight of Hand

However,  D&D Beyond will not add either my Proficiency or Expertise to my Investigation skill, only showing my Intelligence modifier of +3 on the Skills list. I have had to manually customize it as I have found no other way to correct it. Can someone please explain this to me as it seems like a system bug. 

 Post a link to your character.

@IamSposta

https://www.dndbeyond.com/profile/KathydrBing/characters/22031270

So if you remove the Customization the brings your Investigation up to +11 it just gets +3? Is that correct?

Try removing the proficiency and then re-adding it and the expertise again.

Tried removing and adding again, same thing. It only shows my Investigation at +3.  

Do you have any homebrew on the character? Also, when you manually override the Investigation, double check all the skill override fields - when I look at your character sheet, I see that you're not proficient, but I also see that there's some override in there.

Quote from pocketmouse >>

Do you have any homebrew on the character? Also, when you manually override the Investigation, double check all the skill override fields - when I look at your character sheet, I see that you're not proficient, but I also see that there's some override in there.

 I didn’t see any homebrew, but it did list Investigation as one of the four skills taken at 1st level under Features & Traits. 

I reset everything and re chose again. It looks like after I did that the first time I set Investigation to “Not Proficient” instead of “- -“. That seems to have fixed the problem! Thanks for the help you two!