Their transition from an open source project to an organization receiving millions from the Google search box.
The restrictions (based on security reasons) to install an extension from a site different than mozilla addons. For me this was a prequel of app stores.
Mozilla Thunderbird team had no respect for people who reported bugs: they closed important bug reports.
Lack of respect for extension developers breaking compatibility between versions and not clearly isolating extensions. I remember looking into the TabMix Plus extension and seeing ~40 IFs handling special cases with other extensions.
Lack of a good community (circa 2007) where complex questions were never answered.
I can think about more disgusting experiences...