Paint bubbled months later-how to prevent??

So many questions, rust was never an issue, just minor dents and dings. I have a good water seperator in my line that I clean out good before I start any spraying. think I used a urethan primer, I will have to check when I get home. I do know it was not an etching primer. I also did do a pre wash wipe down before primer was applied. I let it dry for about half an hour so no fumes were around and the putty was dry, I only lightly wiped the putty areas so that it did not soak in. The truck bed never left the garage once I started the job, it was on saw horses. I hate to remove the bubbles to see what under them but I know it is not water, I poked a pin hole in one. Will the opoxy or etching primer have a bad effect on putty?