Hmmm...
TOS in the movie era got a little screwy at the end, since most of the crew were command level, but were performing the duties of lower ranking officers so they could stay together.
TNG seemed OK, mostly. Given that Data was second officer, and there were LCDR's all over the ship,
and that Beverly and Troi were commanders, AND because he just

ing deserved it... yeah, he should have had full commander rank.
DS9 would have made more sense if O'Brien had held an officer's rank, like he did on TNG. He was supposedly in charge of the whole engineering crew, but even an ensign outranked him. The officers were just fine, within the usual Starfleet rule that a person can rank up without reassignment.
VOY... yeah, a mess. There were several lieutenants (Ayala, Carey, Durst, among others) who weren't considered senior staff, and an ensign who was.
Since senior staff meetings on Enterprise seemed to be Archer, T'Pol, and Trip... no problems there. While I think Hoshi and especially Travis rated promotion, it doesn't look like 2150's Starfleet used "hollow pip" ranks, so it's possible that ensign rank there constituted LTJG as well. And as for TATV, my head canon is that Riker's holosimulation was not historically accurate.
LD, the big problem is Boimler. In general, if you need to reassign a JG, you find him a JG's post, rather than reduce him to ensign. Mariner's rank makes sense given her service record... Tendi and Rutherford seem to be good officers, so with three years on their belts, it's debatable whether they should still be ensigns, and I expect it's going to get worse.
I didn't watch enough DIS to know what rank everyone was, and PIC didn't really use them much. SNW is still new. And as for PRO, the only question is why a VADM is doing a captain's job.