Agree on where things belong before treating their location as evidence of disrespect.

Most household friction about objects is really about an unspoken system. One person believes there is an obvious place for the scissors and reads their absence from it as carelessness, while the other never knew the rule existed and is simply putting things down. The offence is felt long before anyone has said the system out loud.

Instead of another comment about the shoes, spend ten minutes deciding together where five common things live. Write it somewhere if it helps. Once the agreement exists, a misplaced item is a slip rather than a message, and you can say so without either of you taking it personally.