My guess is that you have multiple Azure AD groups that share the same displayName, haven't you?
As per Atlassian's documentation
In Azure AD, you can have multiple groups with the same name (displayName), but it's not supported in Crowd and results in a failing synchronization. Make sure you change your Azure AD group names to unique ones.
If you were upgrading the legacy app to our new one, you might have run into the error below while trying to authenticate. We're still investigating the cause of this but here's a workaround...
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