Because you've used ply this may be unfixable at this point.
If your ply is decent enough quality that the surface veneer is thick enough to permit you sanding (or scraping) back to bare wood, without sanding through to the next layer, then yes you can fix this. This would simultaneously remove the glue-saturated surface fibres along the joint so that you could get a good stain result when you go to refinish. Unfortunately it's doubtful the plywood does have a thick enough face ply.
Side note: it's hard to tell for sure from the picture but this plywood may benefit from using pre-stain conditioner before staining (see previous Question).
For future projects, while wiping up glue squeeze-out is perhaps not the ideal method (wide range of opinions on what is the best method, see Note bottom) it can be done with greater care and attention to ensure good results. Some tips:
- Always use warm water if possible.
- Cloth should often not be "barely damp" or "just damp" as per the instructions in so many guides, a little wetter than damp works better almost always. But you must clean up excess water as you go to prevent problems.
- This method will nearly always cause raised grain. Expect it and plan ahead to deal with it after the glue has cured.
- Always use a clean cloth and fold it periodically during wiping operations to expose fresh fabric with no glue already soaked into it.
- Be methodical and thorough, do not expect that one wipe down the length of the joint will be enough.
- For squeeze-out on inside corners an old toothbrush is a boon, it can help greatly in getting the last traces of glue from right at the joint line that the folded corner of a cloth often misses.
Last but not least:
- Expect the cleanup to take as long or longer than the joint took to glue and assemble. Having this kind of timeframe in your head at the outset will help ensure the job isn't rushed.
While wiping does sometimes lead to this sort of problem the methods that rely on letting the glue dry partially (to a sort of rubbery consistency, when it cab be picked off with the fingers) or fully (when it can be scraped, chiselled or even sanded off) are not perfect either. In both of these cases wood glue can penetrate into the surface wood fibres and removing the visible glue does not always get all of it, leading to exactly the same problem as you've experienced, albeit on a more limited scale.
Another issue with scraping off glue that has fully dried is that it is bound strongly with the surface wood fibres, and on splinter-prone woods this will inevitably lead to tearout. It's not the ideal method for use on plywood either because of the thin surface veneers common to modern material (even where it is of good quality), which can be physically ripped free as you scrape.