Yes, we have had this happen once at a clients site with BizTalk 2013 R2 CU1.
No, we have not got a root cause for the issue yet, it has only happened once.
Now I'm going to answer you unasked question, "What to do about it?".
One of the first steps to do would be to ensure that your BizTalk server is updated to the latest Cumulative Update, currently CU4 (see kb 3167705) but you should always check what the latest CU is here, kb 2555986 Service Pack and cumulative update list for BizTalk Server. This is what we are going to recommend to our client even though we could not see a particular fix in the updates that mentions this particular issue. This will then allow you to raise the issue with Microsoft if the issue persists. If you didn't do the CU first, one of the first questions Microsoft asks is "What CU are you on?" and if it is not the latest one that would be the first thing they ask you to do.
Meanwhile to address the problem you may want to change the polling statement in the Receive Location to call a stored procedure in the database that contains the logic to say if it should fetch any data or not, in your case only between 9 am and 9 pm. I know it goes a bit against the grain to take that configuration out of BizTalk and into the database or to duplicate the logic database, but it would ensure that the rule is enforced.
In our clients case we only want to allow it to get data once a day around a certain time, so we will probably* have it store the last date data was fetched, if that date is set to the current date the polling stored procedure should return zero rows.
- I'm not the tech-lead/developer for that particular client, so this is just my opinion.