I've not seen or heard of this issue - did you check any logs you take, relating to your script, to check whether the call to that Network got a 200? Should also appear as 'via API' in the Org > Change log
Did you try making the change subsequently in such Networks, either via a single call or in the Dashboard itself?
If this has happened more than once, is it the same Networks that aren't getting updated?
Ultimately, you may need to raise a Support case for this, in which case gather as much info as you can as to when the call was made for the Network(s) in question.
Are you taking steps in your script to ensure you didn't hit the ceiling on call rate?