re 480 on 4:3 TV for NTSC regions is the limit, PAL go to 576 (although overscan does come into it).
As for reasons it can be a few things.
16 pixels is the standard size for a block using current encoding standards (see mod16).
My guess then is the frame shifts at some point during the video, was the victim of a bad transfer (these early 90s cartoons were made in some really odd ways; worse than a lot of anime so getting a good transfer takes some serious effort and skills*) or has some noise there and the app you are using to encode detects this as part of the image, thus when it comes to crop and/or resize it it rounds up to the next 16 so as not to lose the "image". Your TV/DVD player will usually crop though and as it is only those who would transcode it that have a problem.....
*not wanting to knock the DVD makers but they usually concentrate of not messing up the pulldown or fixing problems involved with it. As computers capable of dealing with video at any sensible level were not all the available during the 90s I guess it is a telecine job or worse a copy of the film a TV station had floating around (which could mean any aspect ratio imaginable) which trickles down to this.
Next up is related to the above but is more of an encoder issue, the pixels could well be an odd shape and the correction used changes it as above with the same mod16 coming into play.
All of this is theory though so in the end, test a small section and then a combination of a shift (crop and add borders), a crop and possibly a resize will sort you out.
A shift of 2.5% (2.5% is assuming you lose a full 16 pixels (straight up crop, no resize or testing) where I suspect it is going to be 3 or so at most and if you do it properly there will be no change) is not going to be all that noticeable.
Also is this the 90's version of batman (intro: http://uk.youtube.com/watch?v=lEx9r5enZsk
) and if so is this the box set that got released a few months back? I have been thinking about picking it up and wondered if they made a good transfer.