Hi, I'm not sure I understand correctly, but if I do, I don't think there is a problem. To be more specific (assuming I got the description of problem correctly), there are basically two states of the defender's trebuchet: unloaded (with the arm up—picture 1) and loaded (with the arm down—picture 2).
On both pictures, the trebuchet is rotated to the correct position for destroying the attacker's trebuchets. Now, as an attacker, I did some tests and I was able to destroy the defender's trebuchet with both left and right attacker's trebuchet, no matter if the defender's trebuchet was loaded or unloaded. For the left trebuchet, the power is 25, and for the right trebuchet, the power is 24. From my own experience, you can also destroy the defender's trebuchet while it's being loaded—that means while the arm is moving.
The reason why the attackers usually fail to destroy the trebuchet is because the power is being set too low/high and because they do not rotate the trebuchet correctly. As a result, the attackers do not aim the trebuchet on the top of the tower but rather the wooden floor on the top of the tower or the tower itself if the setting is too off—
picture 3. So, in most of the cases, the reason to fail isn't some bug that causes the thrown stone/barrels to fly through the trebuchet and do nothing, it's more likely the rotation or power being set incorrectly.
Yes, setting up the trebuchet can be tedious sometimes but if you intend to destroy the defender's trebuchet, you just have to use the "b" key and set the rotation more precisely. It really does work.
As far as the tower itself, if you intend to destroy it, it's way better to aim the outer walls instead of the top of the tower—
picture 4. It does work as well. Remember that the HP of the tower has been increased slightly so 5–6 stones are no longer a sufficient amount to destroy it.
As a side note, since the attackers spawn near their trebuchet at the beginning of the round, it is usually not that hard to destroy the defender's trebuchet before their operator even manages to load it; even more so if they have two trebuchets.
Feel free to ask further questions if I misinterpreted the original post.
Cheers, Lenna.