When my players place down a shopkeeper egg it spawns a normal villager called shopkeeper. When they select a container and place the egg down they get a shopkeeper and a villager called shopkeeper.

The Shopkeepers plugin usually cancels the vanilla villager egg spawning. So my current guess would be that maybe one of your other plugins is undoing this cancellation.

Please try to reproduce the issue without other plugins and then step-by-step re-add plugins to identify which other plugins is interferring.

You can also check the https://github.com/Shopkeepers/Shopkeepers-Wiki/wiki/Known-Issues wiki page if there are any plugins listed there that you are using and that might explain this issue.