Hi Chris,
Bondo work takes a lot of practice and patience. Patience is the key. It's hard to say what went wrong without seeing it, but you probably need to spend a little more time block sanding. maybe one more wipe of putty and a final blocking.
If I have to do a lot of plastic work, I like to use a high build primer, and then block sand the primer with 400 grit. Sometimes I use 320 then finish with 400 if I have a lot of blocking to do.
One thing to keep in mind, when you run your hand over your work, if there is anything that you can feel, youre gonna see it when it's painted.
That always tells me I need to spend some more time on it.
If you are new to body work, the best way to learn is by hand, using hand board files and hand blocks.
It all comes with practice and experience.