I used to get this all the time from my VM. I now no longer get it.
It could be related to RAM usage. I was previously running out of RAM, so I enabled emergency swap (Swappiness=1), but a reboot at some point resulted in it being used far more often that it should have been (I had not saved the swappiness setting correctly). This resulted in the server being slow and struggling due to excessive disk accesses. Eventually I spotted this (with the help of bytemark support) and fixed it.
That combined with the improved lower memory apache logger may have contributed to no longer getting the prosody warnings.
That may all be irrelevant, but might might point you in the right direction.
As mentioned above, it did not matter. But it might have been a symptom of my misconfiguration.