Asktually I believe it was never 100% said that they shot Maria in SA2. Only that she died in an accident. Gerald gets shot thought. In Shadow the Hedgehog they show Maria getting shot. Seems like this sonic movie is a mix of SA2, Sonic Heroes and Shadow.
In the adaptation of SA2’s story in Sonic X, they straight up say that Maria was shot and killed.
Was that cut in the US/International version? I remember a bunch of weird changes in Sonic X besides Chris being there.