I'll try to help, even though it's probably been over a year since I last played Atomsmasher.
The two scientists will head for a bomb in a crate once you approach them with the enemies killed. After that they should dissapear.
An easy bomb to miss is one in a room along the long hallway. There are two red windows at one part on each side. Go into the room on the right and spin the wheel there. That'll let you safely go into the other room. In there, use the control panel to pick up the bomb with the crane, and drop it into the hole on the right.
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