Yes, I've definitely had plugins hang around after uninstalling their package. The often happens if you had a previous version of the package installed, but I think sometimes it happens without that. It depends on how the package is written.
InheritResourceGroup would be by far the most likely culprit.
Look in the modx_site_plugins table in the DB to see which ones are still there and whether they're disabled.
If you make any changes there, delete all files in the core/cache directory (or install and run CacheClear).
Another possibility is a mismatch between the various date/timezone settings (MODX, PHP, MySQL).
You could also have one or more invalid modResourceGroupResource objects, though I think that's less likely.
SiteCheck will check both the date/timezone and all the modResourceGroupResource objects for you (along with a lot of other things).
http://bobsguides.com/sitecheck-tutorial.html