While I've looked into a similar post I made here years back - I have the same problem of illustrator. Seems anytime you go to add a rounded rectangle either with their selector or to modify a square edge rectangle it committs this acts -- in effect transforming a 38px by 40px image into 113px by 115px all on its own when saving for web.
If this is a "bounding box" that's been added I don't know, but it seems to be invisible.
Tried selecting it, going to object and then ungroup, which only worked a single try. Apparently there's no clipping mask to release.
How does everyone across the planet using the thing tell Illustrator to bring it back to the actual, intended size? Am saving as .ai and then .gif for the web.
Wow I remember Illustrator 10, I think it was my first real introduction to Illustrator as opposed to Freehand. It is pretty old now, it was released in Nov 2001 and one of its notable features was... Save for Web. As such you may struggle to find an answer to this specific question I'm thinking. It may be a case of reading up on the features and making sure that it isn't something simple that you are overlooking. I'm assuming that you've exported regularly before and this is a seemingly new problem?
As for the dimensions, if it is transforming the entire selected artwork, most of the Save for Web have the ability to set custom dimensions for the exported file size. I don't expect this is a new feature but a fundamental so I would expect you could alter it in the settings panel for the file export.
Sorry I can't be more help. One of the other possible solutions is bringing the artwork into Photoshop and doing your export for the web from there.