It's probably a lag issue. When you're playing, your local copy of the game is saying you broke it, but the server says it's not broken yet, so it reappears, then your previous block break registers, so it disappears, then drops. You can try lowering your rendering distance in video settings - this will reduce the bandwidth needed to play and possibly update things more smoothly with the server.
I don't know if Yogcraft has this item, but there's a rather expensive mining tool in Ultimate called the Vajra that I've noticed seems to cancel this issue out 100% completely, all the time. If I try mining with a pick when I'm lagging behind my server, it will do exactly as you described. When I mine with the Vajra, however, the problem disappeares because the Vajra breaks every breakable block in the same amount of time - instantly. Using a Vajra in survival is actually faster than creative mode block breaking - seriously.
The bad thing about it is that it's a complicated and somewhat expensive recipe, and it uses 2 million EU on a full charge, I think, but it's definitely worth it. If you're having trouble and this is bothering you that much that you can't handle waiting to get enough resources to craft a Vajra, I would honestly just enter into creative mode and give myself a Vajra to compensate for the issue - and I'd do the same for any of my users if they were having that issue. If you don't have Vajra available, a pick with a high efficiency enchantment should make the time spent a significantly more bearable.
