It is at least very common.
It's also important to understand, that our emotions are "warning signs" our body gives us that something is bugging us. They aren't always "right". Sometimes we have panic attacks for example about something that isn't REALLY dangerous. Also, people "fall in love" with people who treat them like crap. So our emotions aren't always "correct" in terms of the messages that they send us.
I try to think of emotions as signals (like stop lights) that are often flashing, but they are not actually aware or conscious of what is actually going on around them.
It is definitely common to run into emotions that run opposite of what you think you want. This doesn't just all of a sudden disappear when you are poly. Nor do you necessarily work through the emotions and they never reappear.
There are still times when I think "WTF this is so damn much of a pita-why am I bothering?"
But most of the time, this is a reaction to a specific circumstance that isn't ACTUALLY a poly issue. It's usually a time issue or distance issue or space issue. Which could arise regardless of poly. So if I take time to actually consider it, break it down and look at it from all sides, now I find that most of my issues aren't really "poly" issues. Its just easy to toss it all under that umbrella.
Jealousy/possessiveness. These aren't poly issues. These are insecurity issues.
Envy is a "not getting your needs met" issue.
Each of these issues can be worked on in the framework of poly, and poly makes them more difficult to ignore than monogamy. But they aren't actually poly issues.
Does that make sense?
"Love As Thou Wilt"