No point contacting eBay, those reminders are sent out automatically and yes sometimes arriving at the most inappropriate times. It's just a reminder and there are 60 days to leave feedback, and only if you wish to, as it is completely voluntary.
You can select not receive those untimely reminders if you wish, just go to your Site Preferences >> Communications Preferences scroll down to the Edit option beside this:
General Preferences
Feedback
Edit your Feedback notification preferences. Be notified when you need to leave Feedback or Feedback is removed.