We've recently completed our 8.5.3 migration to 9.0.1fp4 and we're seeing this error on our servers as well, but only those where roaming profiles are stored. It is happening only on the names.nsf in the roaming directories, and not on every one of them, only some of them.
I have created a new replica with no success.
The design of a database with the errors and one without the errors appears to be identical. Same views, with the same time-stamp and signing authority.
Running "updall -R" on the database initially reproduced the error in DDM, domino console showed the following, indicating that the view had never been built:
09/18/2015 10:43:57 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($AccountsByType)')
09/18/2015 10:43:57 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Accounts)')
09/18/2015 10:43:57 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Adminp)')
09/18/2015 10:43:58 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Certifiers)')
09/18/2015 10:43:58 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Connections)')
09/18/2015 10:43:59 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($CrossCertByName)')
09/18/2015 10:43:59 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($CrossCertByRoot)')
09/18/2015 10:43:59 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($EmailAddresses)')
09/18/2015 10:44:00 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Locations)')
09/18/2015 10:44:00 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($MailGroups)')
09/18/2015 10:44:00 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($PeopleGroupsFlat)')
09/18/2015 10:44:01 AM Informational, rebuilding view - no container or index (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Programs)')
09/18/2015 10:44:01 AM Informational, rebuild view needed - invalid collection header (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($ServerAccess)')
09/18/2015 10:44:01 AM Invalid collection data was detected.
09/18/2015 10:44:01 AM Informational, rebuild view needed - invalid collection header (reading d:\lotus\domino\Data\roaming\<username>\names.nsf view note Title:'($Users)')
09/18/2015 10:44:01 AM Invalid collection data was detected.
After that ran however a further "updall" on the database produced no further errors.
Conclusion? Not entirely sure, but it appears that the error was showing up only on db's where the view index wasn't built. Understandable to a degree, but highly annoying. Hopefully the errors are truly gone and simply will not re-occur tomorrow.