To the OP's original question, 'issues' is somewhat vague - taste difference and safety are two different issues.
I figure if my bucket smells of glorious dry-hopped brew for a week after I clean it, then it probably has some minor effect on taste or aroma. That smell came from
Somewhere and as such was taken from the beer I just bottled.
That said its a big PITA to dry hop in a Carboy.
You guys ever put cereal into one of those plastic Tupperware type deals? My kids Cheerios come out of that thing tasting like crap.