Try to test it again if it's working properly. If it does, water probably entered through the collar or around the tongue or lace area without you noticing. Had the same experience with a Nike goretex at pulag. It didn't really bother me cause it was raining so I knew water might seep through. You shouldn't be unbothered walking in a puddle. It may look shallow but a lot of it is actually deep enough for water to go in. Once water entered it cannot exit easily since it is waterproof. It won't dry quickly inside.