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I have the same view with the same filters I re-use for different taxonomy pages, yet sometimes this error is diplayed.
I can't get the error message/ warning message to hide, even with error reporting set to only log messages. Even third party modules like Disable Messages can't prevent the message from showing to end users. I think that's a bug in itself, but I'm not sure what the message itself means.
1 - Improve the message shown to users when the filter's number of options have been limited by the module.
2 - Instead of a hardcoded value, use drupal_get_variable so that users can customize this setting in a variable, or even better, expose this as a setting in the filter's configuration.