I've seen that too. All I could find on game saves being corrupted is that it is far more severe on the PS2 port of the game.
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MEGAGLITCH 2.0 - WARNING: This glitch can cause massive damage to your save file if you are not careful. Sometimes when you start up the game, it will suffer from a huge bug where all three of your in-game saves are corrupted and have 0 tokens, erasing your current progress and making you not have any cheats discovered. Loading up one of the three corrupted files will result in a worse variant of Begin Without the Subway Token where you start a new game with no items or weapons(besides the close range attack), have 5 health as though you had died whilst leaving a level(see above for more info), have no cursor, and, despite not having collected a single token in the game, always have a message on the screen that says "You got all the tokens". Oh, and since you don't start with the pistol, picking up any weapons in the game will remove the close range attack from your list of moves forever, forcing you to start a new file in order to get it back. You can still complete the game normally despite this(all the levels in the game have been unlocked for you to try them, though you can't complete The General's Lair due a bug from previous ports returning via this glitch, and The Bad Place for reasons seen below). Just be careful-sometimes, the game may suffer from part of a similar bug seen above, leaving a flea level after you die may cause some buggy events, and worst of all, entering The Bad Place will trigger an enormous glitch where the end-of-level cut scene will play as soon as the level begins, causing the game to lock up(and it will continue to do this for an infinite amount of times until you delete the file, should the game auto-save).
However I did stumble upon a reddit post pretty much telling you to do the second thing I listed off in my last post.
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https://www.reddit.com/r/dreamcast/comments/2dod46/fur_fighters_vmu_corruption_problem/
I don't know man. That's all I could read up on your problem.
Edit: There are a lot of save data glitches that run rampant on multiple ports. The Dreamcast has like a handful of them that may make or break a game. The PC port has some too, but the worst I have seen form that is only can be recreated with more modern hardware. My PC might be able to achieve all of the game save issues that plagues the PC port. The PS2 had most of them patched except of that one I quoted which pretty much explains why the PS2 wasn't an easy console to program for. There is an IOS port which I haven't looked into, but I assumed it might be graphical, scripted sequence breaking, and some nuisances that has to be dealt with.