See this about dictionary issues on 8.03 to 9.01 updates.
Also, if you are doing LDAP sync now, it has totally changed and you may need new firewall rules. Sync is gone, instead each scanner directly talks to LDAP. I recommend enabling LDAP over SSL. Watch out for cache errors in the logs (eviction notices). If you see this you need to up your LDAP cache size.
Existing compliance policies that use incident folders will create two folders (incident and quarantine) during the 9.0.1 upgrade. You'll need to review your content policies and decide which you really want.
Read the section on command line tools, they have been reworked.