This happened with the 3GS (which should have been 4), and has continued since then.

The iPhone 4 was actually the only iPhone with a number which coincided with the generation; before it, there was 2G, then 3G, then 3GS, then 4. If anything, the 3GS should’ve been called the iPhone 3, but they’ve been pretty clear from the start that the name doesn’t really reflect a simple incrementing version number.

The also went form the original to 3G. 3GS was actually #3.