The plasma and flamer upgrades for tactical marine squads are supposed to be mutually exclusive, however I found that I could get both on the same squad if I pressed the hotkey for both at the same time. The upgrades would complete sequentially, leaving the squad with plasma guns and the ability to use the flamer.
I originally encountered the bug when I had two squads selected, and wanted one of each, however during the course of the game I found that I could reproduce it easily with one squad selected.
This was originally found in a 3v3 on Solarian's Gate, though I have reproduced it in a 1v1 custom game as well. The timing doesn't have to be exact, I found it possible to activate one slightly before the other to change which upgrade would finish first.
Link to a screenshot of the bug in action