Currently, if the enemy gets anywhere near cover, it switches off, and you need to quickly click on it when the enemies are killed. This seems needless.
I suggest keeping the cover switched on, until you click on it again. It can be coloured red while enemies are using it (or have a red X over it or something), to show you can't use that cover.
There have been a couple of cases where my soldiers didn't get to use cover, due to my forgetting to switch it back on.