Yes. Connectors like USB and headphones consist of metal "fingers" in a plastic insulating shell, perhaps with an outer metal shell. The contacts are sprung and need to move. So the simplest, most natural implementation has gaps around the contacts. There's also usually a thin gap between the connector on the PCB and the outer casing of the phone. If you want it sealed you have to add gaskets everywhere during assembly.

Not to mention sockets for SIM and SD cards. If you can take the back off the whole phone to change the battery, that makes it a lot harder.

Quite a few phones are waterproof or splashproof : http://www.techradar.com/news/best-waterproof-phone

Exact meaning of ingress protection "IP" ratings: http://www.dsmt.com/resources/ip-rating-chart/

Or if you want something cheaper: https://www.gearbest.com/cell-phones/pp_602673.html

Many ports, and notably headphone jacks, have springy pieces of metal inside to clamp onto the plug. This is what causes scratchy audio when you wiggle the plug in old devices, the clamping force has weakened.

Don't things move inside them? They are pretty hard to make water tight.