I can confirm the bug - and is there, eating our hard worked materials, for a long time....
The only way to get around is NOT to use the mouse when you select the effect, but yes, the keyboard ....
I was robbed by this bug at least a dozen times, sadly - like the OP here I thought was some lagging input - but after I changed the mouse 2-3 times - the bug still persist.
True, is not always, but now I am too scared to choose the effect using the mouse - always keyboard and ONLY keyboard. Better be sure....
The same crazy bug affects the rail guns - I use a pair of them or even 3 or 4 Imperial Hammers in many ships / builds - many times with different effects on them - and several times one of the guns only shoots after 2-3 even 5 seconds later, after I press the fire button..... Only 2 of 3 guns fire, or only one of two.... the other will fire only after 2-3 even 5 seconds !
Really, really annoying, that's sure...
Obvious this will ruin your aim, since the target is not there anymore, and is annoying like hell... I did everything - disable - re-enable the rails, log out, restart the game, the PC - no results... only get rid of the bug when I went in the other system.
Many in-game bugs are related to a specific system - remember those engineer planets where you get "frozen" in the jump sequence ?.... when the counting starts, the jumping sequence animation starts, and will keep minutes and minutes there - and only a hard kill of the game will help ?
Some systems are also losing the frame rate and induce a terrible lag if you stay there more than 45 minutes / 1 h, shooting pirates in ResH or just simply doing your mining - the only way around is to log-out and log back, obvious dealing with new pirates if you are mining ....
This is a clear sign, imo, of memory leaks in the game design, in those systems - not really a huge issue, but nonetheless annoying....