Ok, I built a ship with alot of boarding parties...

[QuarianRex]

Also note that the boarding attempt is made before weapons are fired. What does this mean? shield regenerators will make a ship invulnerable to one-on-one capture attempts. This is because the targets shields always regenerate a bit before you can board and you have to wait till next turn before you get another board attempt. Viscious circle ain't it?

So always make sure that you have at least two shield depleter boarding ships (or at least another depleter equiped ship) so that you can tag-team and get past that annoying glitch.