Some of my players have the group default in addition to other groups. Is this normal?
People on Discord told me that players only have the default group when they have no other group assigned.

Example of user with default group:

lpb user ExampleUser info
Parent Groups:
 > default
 > ultimate10  (server=survival)
 > vip

If this is not the expected behavior, how can I go back to a consistent state?
What would happen if I ran a bulk-update command to remove the permission group.default for all users? Would that fix it or could it cause issues?

I've imported my database from PermissionsEx.

That would fix it.
Also players have the default group either when no group is set or they have set it manually.

This shouldn't cause any issues, but you should be able to safely remove default as a parent to players. As long as one of their other groups inherits from default somewhere down the line, they will still have those permissions anyway.