Hiya Regina
No, you are not messing things up.
I would always point everything out to the customer, even if you write them down in a report when you hand the Quotation in. This would be part of your cleaning survey. This i feel shows you are a professional, plus writing things down such as a cracked window BEFORE you clean....shows you were not the ones who broke it!! Thus not liable for replacing it.
Even during the cleaning process, when we clean new builds, anything we find damaged gets written down, otherwise when checked by the client after we have gone, they will assume my cleaners have done the damage. It saves a lot of grieve.
Kind Regards
Tim