Hi @Fraesp87
In order to reclaim VAT from HMRC you must be able to show - if asked - that it's correct.
The only way to do this in practice is to have a physical/electronic copy of the supplier's invoice. The supplier's invoice must show their VAT Registration number & the amount of VAT charged on the transaction.
If you do not have this (or cannot prove that VAT was actually paid to the supplier in some way) you should zero rate the transaction no matter what QBO thinks. After all, it's your neck on the line if/when HMRC checks up.
Hope this helps.