Yes, in fact you noticed one of the remaining flaws in the reaction-fire code.
The current reaction-fire system runs a test before actually firing to determine the likelihood of hitting the enemy (it even factors in friendly fire likelihood). However it simply tests the pathway from the weapon to the center of the enemy. If there is an obstacle in the way (e.g. a window ledge) then the test may come up negative... i.e. the chance of hitting the enemy is too low to bother reacting. The calculation also doesn't take into account splash damage so again even reaction-fire with a RPG may result in the same problem under these circumstances.
One solution is to "scan" the enemy in this code, testing other points besides just the center. This still won't taken into account splash damage effects properly but I'm confident this can be worked into the calculation as well.
I also think sub-grid-point accuracy aiming should be allowed in general in the game... it can be done but will involve a bit of work.