You will see the “Logo Incompatible” note when a logo is applied to an item that does not support that decoration method. Please, make sure the correct logos are applied to the items in your store. If the logo is labeled “PRINT ONLY” in the store's logo bank, it should only be applied to the items that will get their logos printed. Same for logos labeled "EMB ONLY", those can only be applied to items that will have the logo embroidered.
If there is no decoration method noted below a logo, it is viable to be applied to both printed and embroidered products. You can filter the items by “Decoration Type” to see which items will get a printed logo vs an embroidered one in your store.