There are several limitations associated with Office 365 group site collections.
You cannot activate custom scripts on OneDrive group site collections. For full details on this, see here.
You cannot modify a web part for a form, list, or library. The only exception is InfoPath forms. Sharepoint will not be able to detect whether a form has been modified, which may result in an error.
Nintex Forms (for Lists)
Nintex Forms for Lists cannot be migrated.
You cannot migrate document templates.
SharePoint Designer Settings
SharePoint Designer settings cannot be migrated. This is because you cannot connect to Office 365 group site collection through SharePoint Designer.
The Sharegate Server Extension cannot be installed on Office 365 group site collections. This means that all features that require the Server Extension to be installed will not be available.