I have rented motorbikes in Thailand dozens of times, in Chiang Mai, Chiang Rai, Mae Hong Son, Pai, Udon Thani, Koh Samui, Pattaya, Phuket and I have never ever been scammed. I have been late with several hours when returing (phoned the company and told them of course) I have been extending the rental period while on the road several times - I have rented all kinds of bikes, scooters, 250 dirt bikes, big bikes, shoppers - never ever had an issue with anything! I broke a indicator on a dirtbike I rented at POP in Chiang Mai and was sure they gonna rip me off but they only charged me 2-300 baht for that.

But of course - its a good idea to take many photos of the bike before leaving the rental shop and also in front of the staff there so if they have the slightest idea of scamming you they will have to think twice.
I have several times seen all kind of tourists and backpackers treating their rental bikes like shit, doing "burnouts" towards a concrete wall, wheelies with a 250 dirtbike etc - so no wonder the rental companies get a little wary at times.
Keep away from the worst backpacker crowds and the places they visit and you will be fine.

Ted: Long distance bus stations in most bigger cities in Thailand are placed outside of the city center, often by 5-10 kms. Thats not a scam, its a thing done for conveniance for both passangers and bus drivers. Who wanna spend the last 30-60 minutes in a bus in mean city traffic that hardly moves at all. And doing 5-10 km/h in average.

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In the end everything will be fine. If its not fine its not the end....