Check the Clipboard Handling preferences in both InDesign and Illustrator and see if changing something there makes a difference.
Also, you mentioned that it's "only from recent update". Does it mean that you don't have this issue with the same Illustrator file when copy-pasting to InDesign 2025?
I know you want to copy and paste EPS as before, but EPS is really outdated file format and has only been supported for legacy files for a long time.
Do you have to keep EPS format - can you save as .ai? Or is that too much work.
Besides the warnings above - here's the alternative advice if the above is not good for you and your workflow.
It looks like this is a latest InDesign update. The “EPS Import: UnmatchedMark” message is tied to how InDesign translates clipboard data from Illustrator. Illustrator places several formats on the clipboard (PDF, SVG, EPS, WMF), and InDesign chooses one to interpret. Something in that chain is breaking since the update.
A few practical workarounds until Adobe patches it:
1. Use “Paste as” → AICB
In Illustrator: Preferences > File Handling & Clipboard
Enable AICB (no transparency) (or with transparency if needed)
Disable PDF clipboard temporarily
This forces Illustrator to send the older, simpler clipboard format. Many people report this avoids the UnmatchedMark error.
2. Try “Paste in Place” instead of “Paste”
Weirdly, for some users one works and the other triggers the error.
3. Roll back Illustrator or InDesign
If copy/paste is essential to your workflow, rolling back one version of either app restores the previous clipboard handling.
(I never update to the latest version of anything - including Adobe Software, I have the latest installed, but I use 2023 and moving to 2024 soon).
4. Report it as a confirmed bug
Adobe engineers do monitor the UserVoice/Bug pages more closely than forum threads. Multiple reports help it reach priority.
This is a valid workflow and it should work copying vectors from Illustrator to InDesign is used by loads of people. At the moment it might seem broken because of the update, not the workflow. Hopefully Adobe patches the clipboard interpreter quickly if it's the cause.