There are several contradictions in Maiden.
For one, it states that Aerith fell in love with Zack at age seventeen.
Zack put on sad face as if he was sulking but then smiled carefree. It was the unchanged smile that Aerith knew from when they were young. When she was seventeen, it was what attracted her to him.
But Crisis Core shows us she fell in love with Zack at age 15.
In Maiden, Aerith is shocked to know Zack died, but we know that in CC, she felt and knew Zack had died. It's a very important aspect shown in the ending.
Hojo is shown within the Lifestream and then absorbed by Sephiroth. However, Hojo did not immediately die after his defeat from Cloud and the others. With his dying strength he uploaded his consciousness into the Shinra Network. He didn't die until after the defeat of Sephiroth in the Northern Crater. Not only that, but DC explains that Hojo injected himself with Jenova cells not just for his scientific curiosity but to become a vessel for Omega. Again, contradicting Maiden and his fate of being absorbed by Sephiroth.
Maiden states that Aerith rallied the entire Lifestream of the planet to stop Meteor, but the description of events in the 10th Anniversary Ultimania of FFVII states that she rallied a segment of the Lifestream, not the entirety. Again, another contradiction.
Finally, Zack states he taught Cloud Omnislash in Maiden and it was one of his moves. But this isn't shown at all in Crisis Core, and there's no time he could've ever taught Cloud that move, seeing as how he used a gun. Furthermore, Omnislash is never described as a move originating from Zack in its definition in the CC Complete Guide and is specifically called a limit break unique to Cloud. Another odd contradiction. Of course one could say Zack was lying but it seems rather weird.
Those are some of the most glaring inconsistencies with Maiden right there. Those, coupled with its exclusion in every subsequent chronical of events of the Compilation of FFVII, and its events even being excluded in Aerith's 10th Anniversary profile and exclusion in the list of entries of the Compilation of FFVII in the FFVII 10th Anniversary Guide and CC Complete Guide pretty much shows Maiden isn't canon.