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This morning I had to go to Phnom Penh and Giant Ibis bus company had all the seats booked. Normally there was always space, but due to high season, the bus was full. However, they were very nice and when they couldn't get me a seat with their competitor's Mekong, which was also full, they allowed me to ride on an extendable seat that blocks the path in the bus. For which I was enormously grateful, so I 'wai-ed' the girl at the desk 3 times with hands very high, and her smile died for a moment. It felt like I have done something inappropriate, although we have been very informal at that point.

Is it inappropriate to 'over-wai'? Or to joke about 'wai-ing'?

Wai and similar gestures are used to greet and show respect in many parts of South and East Asia:

The Thai greeting referred to as the wai (Thai: ไหว้, pronounced wâi) consists of a slight bow, with the palms pressed together in a prayer-like fashion. It has its origin in the Indian Añjali Mudrā, like the Indian namaste and the Cambodian sampeah

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Sampeah (Cambodian greeting)

Farang tourists usually don't wai properly, when they do. They're usually quite awkward, and hand placement and movement are usually incorrect, or awkward at best.

Waiing is also considered in Thailand, Cambodia and Laos an insider's thing. Foreigners are not expected to, nor expected to know how to.

Waiing high three times is weird, at best. That would be something addressed to a monk, maybe. Keep it simple. A single wai, a couple of seconds, mid-height, is enough. Or just a simple thank you.

In Thailand, there's a superstition that wai'ing someone younger than yourself takes a year (maybe years?) off of their life.

A couple of times when I have wai'ed Thai friends that were noticeably younger than me, I was chided (mostly jokingly) that I had shortened their life.

In some places it is rude to wai someone significantly younger than yourself. This may have been a factor as you describe a 'girl'.