I only used it 1 time, after the initial mistake. But it did cause some head scatching. After he signed his name next to the Used stamp I never had any issues entering or exiting.
This happened to me before on entry to Thailand. The officer at the time crossed out the used stamp and put his signature next to it. It did however cause a problem on my next 90 day border bounce, like yourself. He said, he must of thought it was a single entry and stamped used. They checked the computer for some time and said everything is fine now 😉