So I am on a United award with 2 United flights and then a leg in TK from Bru-ist I was unable to select seats either via app or the help desk. I'm within the 24 hr check in window so I assume the help desk will be of no use now.

My question is on arrival at BRU, will we be able to go to the gate and check in there or do we have to go thru passport control to use the check in counters.

Thanks for any thoughts.

you mean you were not able to select seats when checking in for the flights? that sounds unusual.
I would not count on checking in at the gate. TK has a strict 60 minute checkin deadline prior to departure. I doubt the gate will be manned before that time. In many airports chekin staff closes checkin counter and goes to the gate to handle the flight. So when you are not able to checkin online you should look for a transfer desk at BRU (not sure if they exist) or exit airside and check in at the regular checkin counters.
In case the BRU-IST leg is also on your award you should be able to checkin for the BRU-IST-flight at your origin airport. It could be that you can't select a seat there as United and Turkish Airlines use different checkin systems and it has been reported that seat selection will not be possible from a non TK-station.

If this is one 1 ticket, the UA check-in agents at origin will be able to check you in all the way to final destination. You may not be able to select seats yourself, but it doesn't mean that UA check-in agents can do it.

If you are on separate tickets (it is not clear from your post), you should try to check-in with TK (website or app) for the BRU-IST leg. If unsuccessful, you go to transfer desk at BRU. Def. no check-in at the gate as it will be too late/past the check-in deadline.