I have found my soldiers in certain positions in which high accuracy shots will miss a clear shot several times in a row, generally by passing the target along the same or almost the same trajectory, ie. passing by the left side of the target every shot several times in a row.
What you described above could be attributed to the inherent inaccuracy of the weapon (bullet comes out a bit different every shot), unless the misses were almost always going on the same side of the target, in which case it would indicate maybe a positioning glitch of some kind.
I have had high-accuracy misses that went on the same trajectory several times in a row, on shots that were fairly short range. What I found would fix them was to move the soldier a bit and shoot again. I've also never seen it on angles that were a direct orthogonal or diagonal, rather it seems to happen mostly on angles that make a more complicated triangle on graph paper.
If I see it happen again, I'll attach a save file.