I found collision issues in some of my bases too. At least I was able to figure that one out. The ‘Circle Window’, which can be placed instead of walls on a cuboid room.
In this case huge because I have it scaled a LOT!
You can see the part name while I aim at the invisible collision
It is from my Zero Hour base
I then tested regular version, again see target part
No collision on either side of the middle
Visualised with lights placed, after which I continued to my freighter as you have now seen in my previous post
So this collision is just moved and/or rotated it seems.
On the freighter I have no clue yet, but it may be parts of the freighter itself? Not part of the base, as aim tells us nothing.