The only thing I can think of is that the pets you had there might have died somehow. One way to check is to copy your game, since you don't want to waste your resources if this doesn't work. You are going to want to try to use a resurrection spell or book, which might be kind of expensive depending on where you are in your game. If you don't have another way, activate wizard mode in the F12 menu, then use the F5 menu to wish for a book of resurrection. Read the book while you're in the dojo map, and see if the missing pets show up on the list. If they don't, I'm not really sure what you can do since even resetting the map won't help you with the training cost.
To be honest, I just like looking at other people's progress in this game. I also don't believe that you have an actual bug on your hands; instead, I think you merely overlooked something. I'm not a crazy expert on this game, but I figured another set of eyes might do you some good.
That being said, if you're still keen on looking for help on this problem, you can archive your save folder and upload it to somewhere like mediafire, zippyshare, or even that new megaupload replacement site. Provide the link and I'll download and give it a look-see.
im not sure how long u have to play for them to disappear since i was certain they were safe so i just left them for a pretty long time
or maybe its just me >.> which is lame considering i almost screwed up my main quest since i couldn't continue it after i copy and pasted the files.(fixed it by copying and pasting other files with some side effects)
It seems to just be bugged, or not translated properly, as even after taking my pet out of the dojo it acts as though there's still one in there, with the next Entrust being 10k.