The list of supported extensions with ePO 5.0 is available in support article:
KB76736 - ePO 5.0 Supported Products
Please make sure you use the right extensions, although I do find it a little odd how that might corrupt the master repository so it could just be coincidence.
There are also support articles on how to rebuild the master repostory in the event of corruption, but i'm not sure they have been updated yet to account for ePO 5.0.
If this is a test environment it may just be easier to rebuild, ensuring you use the supported extensions. If you get the same result, open a McAfee support case so it can be investigated in more detail.
The Apache message you have posted is not relevant, it's informational and comes from an httpd.conf directive included in the product to disable the Apache AcceptEx() API function on Windows.
You should not change that setting.
All products and extensions were in compatible list (checked before integration) and they were downloaded from Software manager in ePO.
When we tried to use snapshot in ePO. Instalation was rolled back because Apache server error (could not be started).
We will try to replicate problem again and in case of successful replication we will open case.