This is a feature, though I understand how it is unexpected. If a PNG has no transparency and there is a reduction in size via jpeg compression, we will convert the format. Simply put, there were many users bringing in massive PNGs that could be highly compressed, especially for retina devices, causing their site to be slow.
Even if the file format is the same, accessing by name isn't always going to yield expected results with 'automatically optimize' turned on; Hype will often generate a @2x variant and use the original naming as the lower resolution @1x version. Basically if you need to use the resource in code, you should disable the automatically optimize box.