You mean when you get damage from the molotov? Please elaborate.
I've been having a similar problem to - and it's not from molotov damage. You'll tell your unit to do something, and it simply won't. Tell a sniper to fire, and it'll just stand there, or actually run at the enemy (like it was given a move order). Sometimes a mortar is told to fire, and it won't even setup. It'll just stand there.
As for Molotovs, my only complaint is their price. They are simply so cheap, and so much better than rifle-nades.