It isn't you using Confuse that causes the glitch; it's the attacking Moga that uses it. Watch your Moga's life bar; right underneath it is where the Confuse icon will appear if your opponent uses it on you. It has an arrow reversing itself, curving up then down, so watch for it. If that arrow is there DO NOT capture anything until it fades out; if you do it will be lost. You can catch it, name it, etc but it will not show up in your inventory.
I'm going ahead on Nova's quest slowly, not going to buy any more star seeds until they fix the glitches in this game! Every time I have bought them they end up only giving me half what I paid for, so I'm going to wait until the purchase system is a bit more reliable. Not to mention it is no fun to buy the seeds and then end up losing them to a game freeze or some other glitch. So, since I have to harvest seeds first, it is going pretty slow. But, time I have plenty of, and since I have to spend so much time on line loading data lately, and waiting while it either uploads or downloads, I have lots of time to kill... sweatdrop