I FIGURED THE BUGS OUT! (woohoo!)
Okay, so one of them was indeed two distinct timers on the same timer object. Nice one, Newt!
The second bug (explosions not getting set sometimes) is rather obscure but:
I was spawning explosions, setting their positions to a meteorite and then destroying said meteorite on laser collision with that meteorite.
Turns out that sometimes a laser would hit more than one meteorite. This means the actions get run once for each meteorite.... but when destroying the meteorite, Construct destroys the whole matched list of them! So on the next run, there is no meteorite to set the explosions to, and sometimes the runtime crashes.
This one is probably a bug. I got around it by adding "on each meteorite" after the "on collision" condition.... so now for each collided meteorite explosions get spawned and meteorite gets deleted.... one by one.
I hope this was the source of the crashes.... so I can release the game