The irony is that I've recently discovered that my original issue might have in fact been a full on bug.
The area where I was stuck is when you return to level 1 (through natural progression of story) in order to try and break out the other alien with your upgraded skills. There is an area where there are 2 power cores both surrounded by inhibitors (blue walls).
This area is not accessible to you but there are conveyor belts traveling through the area.
In my second attempt (after restart) this puzzle if very simple. There is a bomb to send through the conveyor belt. Impossible to miss this. Timing is the only factor.
But during my original play, this bomb could not travel through the inhibitor as intended. Now that i am further along i have encountered this issue again in a different way.
Now I needed to "Launch" a bomb through a doorway, and it works, but if you die and continue, the bomb will not travel through the doorway, it will be knocked back as if there is an inhibitor there (and there once was).
I have to back out into the menu and continue game to get past this issue, and even then, I only get one shot at this, if I die, its back out to the menu again.
Also, DonJose, that sounds very frustrating indeed