I mostly just want to complain a little, and see if this is something had maybe been addressed somewhere because I know D&D beyond is "always changing".

I was asked to DM 5e at local game store. I arrive and 3 players are using D&D beyond essentially as their only source.

The first is playing a Fighter https://19216811.cam/ https://1921681001.id/- Brute, the second a Changeling, and the third a Dhampfir.

I was taken aback, I don't use the program at all, but does it really not clearly explain what content is core and what content you should ask permission?

The first 2 being UA and the third being straight up Homebrew, I was a little upset because I was not prepared to accept a brute or a Homebrew race. It's hard to blame players, especially 5e noobs who don't understand what's going on.

But I'm a little miffed that D&D beyond doesn't put a huge pop-up window that says "YOU ARE USING PLAYTEST / HOMEBREW CONTENT, ASK YOUR DM IF THIS CONTENT IS APPROPRIATE FOR THE GAME." I didn't want to tell people to make whole new characters, but I really didn't want to deal with non-core content.

Has anyone else noticed this problem with Beyond? How

No sorry I personally follow Unearthed Arcana, so I am mostly updated on what is play test content and what is not. So I definitely do not have have this problem. I also do have them noted as play test content at times when copied in dnd beyond. (Note: This is not published content but saved as a homebrew creation for anyone who either wants to play as the UA version or to simply record it.) DND Beyond is not perfect but it does the quickest and best it can. Maybe this can help you. If you see the Light Blue House Icon in the spell, magic item, subclass, and race then that means its homebrew. Or if it has anything like Version: 1 below its name in the customization or description when toggling the magic item, spell, and such. The Light Blue House Icon can also be found in the character creation builder as a Light Blue House icon, mostly this one is for the races.

The Light Blue House Icon

I don’t allow people to show up with pregenerated characters unless I have already told them what is or is not allowed. I prefer to have everyone create their characters together during session 0 so I can answer questions like this and they can build a team instead of a bunch of disparate individuals. This kind of stuff, discussing what is or is not allowed in the game is exactly what Session 0 is for.

Are you sure the Changeling was The UA version and not the one published in the Eberron book?  There is an official Dhampir lineage, in Van Richten’s. (spelled differently than you spelled it, so maybe the one you are looking at is homebrew).  Brute is odd, because UA has been unavailable on DDB for some time. This is either a homebrew version or this person created that character quite some time ago.  In fact, every example you gave argues against the person in question being a “5e noob,” unless they are somehow connected with an experienced player who is sharing content with them. They would have to have enough experience to know how to homebrew these things, to know how to subscrib to homebrew here, and/or have access to the Eberron and/Van Richten book.

That said, while one can exclude certain categories of sources (e.g homebrew, Eberron, Critical Role, Magic The Gathering) from the builder, there isn’t the fine grain control some of us would like to see. 

All in all I think this is more a case of players trying to get away with things than anything else. Even if it is “noobs,” you could easily see the same thing from players who consulted the D&D wiki to create their characters.