So I've got to level 7 (Storing Sectors) in my replay so far. Btw, I've managed to destroy the main CPU at Control Base! So much easier to proceed now. And though I'm not sure about that, but this action might have an influence on my ability to get to the 3rd secret level.
Now I'd like to report some things that can be regarded as bugs which I've (re)discovered during my replay session by now. The post will contain attached screenshots so that Zaxtor doesn't have any problem at seeking the culprits. So if you don't wanna spoil yourself some fun, don't open them (though they mostly contain Mapster information and no automap shots contrary to the way I'm used to report such things).
Every shot will contain a picture of a buggy (or questionable) place along with signs signifying the mapname (such as ExLx) of the level and the number of the sector/sprite in question.
Attachment #1: A sector that's been mistakenly given the secret lotag. Looks pretty much like you forgot to remove that lotag after copying part of the previous level where the sector is an actual secret.
Attachment #2: Here I have doubts about this sector's properties. The problem is that this energy field (or whatever it is) doesn't kill (or hurt) the player at all. While I think it should.
Attachment #3: Here we got a yeallow access switch that seemingly doesn't do anything. At the same time, it can stop you from proceeding further through the level (you can accidently use the yellow card on it and thus block yourself from getting to the boss battle. Though it also might be intentional (like a trap of sth).
Attachment #4: Here's a computer pad that can either crush you in level's geometry or warp you outside the cluster path in the computer puzzle area (the latter case can be cured with the DNCLIP cheat). At least that happened to me on my first playthrough, and now the game did it to me again. I'm not sure why no one has reported this yet. Probably that's ever happened only in my case. Anyway, looking into Mapster, there's something not right with teleporter and destination sector effectors, like they're kinda misplaced or sth. But the technical part is left to you.
Also I'd like to report a boss slayer problem. Seems that Morphling's and Powerglove's slayers don't tell the player what weapons they apply to. At least they didn't in my case.
That's everything I've found to this moment. Will play further soon. If I find anything else, wait for another report.