Bringing the bag through security
If you have to gate-check your bag and have no option to check it at a check-in desk/ticket counter pre-security, then you'll have to take your bag through security. Unfortunately, this means that all the items in your bag will be subject to security rules and it will limit what you'll be allowed to take away with you.
Having to wait to collect your bag
One of the downsides of gate checking your bag as opposed to carrying it on board with you is that you'll have to wait for your bag at baggage collection. Usually, if you're only taking a carry-on bag in the cabin, you can skip baggage collection, which significantly speeds up the post-flight process.
Not having important items on-person
If you have to check your bag at the gate and aren't allowed to bring baggage with you in the cabin, you might not be able to carry all the items that you need during your flight.
Additionally, if you're caught off guard and are forced to gate check because the cabin has run out of space, you might accidentally leave an item in your baggage that you wanted to carry or keep in your pockets i.e headphones, a book, or in worse cases, your passport!