This doesn't change the simple fact that Israel sites the lack of a building permit as an excuse to destroy anything built in Gaza. (Or the WestBank)
There are far more instances of this, including some where they just pour concrete into the wells. Unfortunately, English speaking outlets don't really report on these incidents. So the only english "sources" that can be found are heavily slanted Muslim propaganda articles.
The other sources are actually reports from the Knesset, which I also can't read without a translator. (Which is why I didn't link either) Specifically, the source I am referencing here are IWA (Israel Water Authority) reports on illegal water well drilling. They release a report every year. They tend to get referenced by NGOs in articles relating to Gaza or the West Bank.
In my opinion, what matters here is enforcement. Israel does enforce their rights on water sources. Even water sources inside of Gaza/WestBank. The lack of targeted strikes in Gaza doesn't mean they don't claim control over all water sources in the territories. (IE: China and the South China Sea debacle)