I opened a thread about copy/paste which I consider to be a bug. Probably a similar situation. Because that too is a problem.
https://illustrator.uservoice.com/forums/601447-illustrator-desktop-bugs/suggestions/43956288-the-colors-in-the-closed-file-are-persistently-and

Support page ... https://helpx.adobe.com/jp/illustrator/kb/plugin-missing-issue.html
But I couldn't find "Microsoft Visual C++ Redistributable (2012-2017) "
There is "Microsoft Visual C++ 2015-2019 Redistributable (x64) " and "Microsoft Visual C++ 2015-2019 Redistributable (x86) "
I don't know how should I treat that.

Thanks, looks fixed in the beta.

This happens to me every time copy and pasting. For example, in many of my documents, I have a pattern swatch and have created multiple copies of the pattern swatch. Each copy will have been changed slightly, like just changing the color.... This operates just fine on anything I build with those swatches. The issue arises when I select an illustration with those pattern swatches and copy and paste them. When I paste that illustration to a new location of the document (or to a new document)... it does not hold the appearance of the pattern swatch, and usually reverts to some other color....

This effects my every day workflow and is increasingly irritating.

I think v25.3.1 is a broken version with some other serious bugs. Roll back to v25.2.3 is the only best workaround.

@monokano, this method worked. I renamed all of the swatches with no spaces as you said. The result was no auto cloning of the pattern. Thanks so very much I really appreciate your assistance. Hope the AI Team can resolve the pesky bug soon.

I contacted the Adobe helpdesk when I first encountered this issue. The helped me roll back to a previous version and put my preferences an a seperate folder. So I could keep them.

Emily,
Unfortunately at the moment the only fix is to roll back to a previous version. Beware tho as you will lose your preferences when doing so. I understand your frustration. It happened when I was doing tech packs too. So annoying!!

To work around this bug, remove the space character from the swatch name.

Emily, install a previous version to finish your work.

Does anyone have any idea when this will be corrected? I am copying/pasting socks with pattern fills from one file to another... On a deadline for completing Tech Packs and CANNOT recolor 200 socks!!

Since last week's update I am having the same problem myself. I'm on 25.3.1, Mac OS Big Sur 11.4.

Hi, I am having this same issue on Illustrator 25.3.1, when I copy and paste a shape filled with a pattern that I have re-coloured, the original version of the pattern is what is pasted, not the version I copied, even when pasting into a new document with no existing pattern swatches.

Having the same issue. When copy and pasting a shape with a pattern fill, it will paste with a different color way. Went to version 25.2.3 and I no longer have the issues. Lost all presets.

I am having the same issue.

I am having the same issue and trying to get a huge launch done before end of day... The one work around I've done that (though time consuming) allows me to do what I need to is to drag and drop the original pattern file from the swatch menu, then copy that to my new document and recreate the swatch. OOF.

Having the same frustrating problem. I work in fashion, have a pattern in multiple colorways and pasting from one file to the other renders the same pattern on the destination file. It worked for me yesterday but with only taking the swatch pattern out from the tab itself and placing on top of the filled path, then copy/paste. It worked only once. uhh Looking forward to your solution Illustrator Team!

I am having a similar issue. I have been doing a series of illustrations using a variety of patterns in multiple colors. Recently, when I start a new project and try to use those patterns, the pattern will work but the colors of it will not be correct. For example, purple polka dots when selected come out yellow polka dots. If I copy and paste any items, the pattern colors change. I am showing a butterfly illustration I am working on and the left side is the original, I copied and pasted that wing, and the wing on the right has the same patterns but different colors. It's extremely frustrating as these are for a client and I have no work around at the moment. I've been sort of limping through the rest of these by not creating a new document (just adjusting the original) and not copying and pasting anything.

The only fix so far after weeks of reporting this is rolling back to a previous version. Which resulted in losing all my preferences. Not happy!

related, plug-in error
https://community.adobe.com/t5/illustrator/error-loading-plugins-recolor-aip/m-p/12161910#M282684