The prototype seems to have been found by people from the Video Game History Foundation, with the director and founder of the foundation itself, Frank Cifaldi, being the one that released the prototype for research and preservation. The prototype was found in a yellow NES cartridge, with a simple label with the message "NOA COPY 2.23.87" "THE LEGEND OF ZELDA" in it. According to the label data, the prototype dates back to February 23rd, 1987, which predates the official release for the NES by 6 months.
Twitter user MrTalida started work on a comparison between the v1.0 official release of the title against the found prototype, with the prototype has quite a bit of differences in several parts of the ROM's data banks, which mostly seem to relate (at a first glance) to actual ASM code from the game according to the game's data bank structure.
So far, the only difference MrTalida found has been a glitch where Link gets stuck into the lower part of the screen whenever Link exists a door or a cave:
Any plausible differences and (most likely) glitches that could potentially be found within this prototype could very well be attributed to beta code being tested for the conversion of the game from disk to cartridge.
Video Game History Foundation website