It would probably help your understanding to know that this exact phrase is widely used in the UK (where Adams was from) by all sorts of official bodies, typically in a slightly perfunctory way, as part of an explanation that something isn't working as it should be.
Here's a google search limited to
gov.uk sites for the exact phrase. Examples:
our roadworks search is not working at the moment. We are investigating this problem and should have it fixed very soon. We apologise for the inconvenience.
Parking permits: Residents won't be able to apply for new resident parking permits until 12:30pm on Thursday 3 June. We apologise for the inconvenience
Our phonelines are busier than usual at the moment. We apologise for the inconvenience
etc etc. What Adams appears to be saying, with his typical dry humour, is that the creator of the universe knows that things aren't working quite as they should be, and is sorry for this (but not that sorry).