I remember going through my diary over and over again to see if there was something I could have done differently whilst pregnant - to stop this happening to my child. I didn't even take a paracetamol during pregnancy just in case.
Warburg Micro Syndrome (WMS) is a genetic condition - you didn't do a thing wrong - it's just one of those things.
If you and your partner are carriers of a WMS gene you have a 1 in 4 chance of having a child with WMS.
The genes associated with WMS ('RAB18 Deficiency') - discovered so far - are RAB3GAP1; RAB3GAP2; RAB18 + TBC1D20 - new genes will be identified in the future and new mutations within these genes are being found all the time but it is a painstakingly slow process.
I guess the analogy 'needle in a haystack' could be used but on a microscopic level ?

Consanguinity ?
As this condition is so rare, chances are you will have been asked if you and your partner are related at your genetics appointment. When you said no you were probably asked again … this is obviously a shock / upsetting but I guess they have to ask (?).
At the moment the majority of confirmed WMS cases around the world are clusters of children born to parents who, mainly for cultural reasons, have married within their own families - often over several generations.
Without these clusters WMS might never have been discovered and we might never have had a 'label' for our child's condition - never finding another family like our own but here we are ...

Martsolf Syndrome
It is also possible that your child may have Martsolf Syndrome - a very similar (milder) condition to WMS but this will become more obvious as your child gets older.