Some menu items become fixed or undeletable

I've not seen this reported to date, so I chalked this up to a bug in my website. But since then I've installed Drupal on three sites, and on each and every one I've run into problems where the menu seems to get corrupted ... or at least behave improperly.

Examples:

1. I add an aggregator category or feed and it automatically gets added to the menu. Okay, that's fine. I'll just go delete it from the menu. But about 1/3 of the time I cannot. I disable the menu item, the page loads with a message confirming that the menu item is deleted. Yet the menu item is still there. If I try to edit the item, all I can edit is the name, but no other settings are available. Additionally, whenever these things happen, the node ID has become a negative number ('node/-162') [On two sites, running 4.5.0 and 4.5.1] Sometimes resetting the menu item will clear it up, but not always.
2. Activating the event module on a freshly installed 4.5.2 website places a "calendar" menu item. It is "locked". Undeletable. Unmovable. Resetting the entire menu does not affect this at all. The only way to remove it is to deactivate the events module altogether.

The sites in example #1 are using clean URLs. Both were initially 4.5.0 installations, db on MYSQL. The site in #2 does not use clean URLs (yet). As yet, I've not tried the aggregator for that site.

These things happen consistently. And they are crippling, for they force (inconvenient) menu items for certain features on a seemingly haphazard basis.