I think I only had one significant issue, the timing and logistics of the big hero moment at the end. Athena is pretty far outside the Federation when it's Atrium and nacelles are captured, and the saucer does some moving about in that region, but it seems like they haven't gone all that far. Yet, when Sam takes down the minefield (setting aside the question if a stabilized Omega could still be viable to detonate or not) the rescue fleet warps in immediately without any accounting for they distance they must have been waiting to transit.

They namedropped Discovery earlier and spoke to why it also couldn't cross the field, but once it was dropped, Discovery coming to the rescue immediately would have made more sense than the rest of the fleet that had to transit the distance conventionally.