Pathfinder Merge actually Dividing, leaving cut out objects behind
This might be easier to read on the forums where the images are inline with the explanation, but I copy pasted everything here anyway. Here's the thread.
This has been a thorn in my side for so long I can no longer ignore it. I don't know when it happened but at some point Illustrator's Merge tool started dividing objects instead of merging them, and leaves behind cut up versions of objects that are behind the visible objects.
MacBook Pro 15 2017
macOS Mojave Version 10.14.2
2.9 GHz Intel Core i7
using Illustrator CC 2019 version 23.0.2
I'm pretty sure this still happens on my windows 10 computer at home as well.
Interestingly, if I have only a few objects involved, it merges just fine, but when I'm working on logos that are even minutely complex it pitches a fit. I've expanded appearance, expanded text, expanded strokes, ungrouped objects, and put them all on the same layer and it still doesn't work. Thing is, the objects I'm merging aren't even terribly complex, and as a test I made 15 rectangles of various colors (some the same and some different) and had them overlapping in various ways.
Screen Shot 2019-03-05 at 4.06.07 PM.png
Here you see the objects selected so you can see the outlines and how the layers are organized.
Screen Shot 2019-03-05 at 4.06.16 PM.pngScreen Shot 2019-03-05 at 4.09.32 PM.png
Here's what happens when I try to merge (you can barely see the gaps that show the color behind themScreen Shot 2019-03-05 at 4.06.34 PM.png
I moved part of the blue area at the top to show the navy object underneath has not been deleted.
Screen Shot 2019-03-05 at 4.14.20 PM.png
So with the objects now properly ruined, here's what the layers look like.
Screen Shot 2019-03-05 at 4.23.59 PM.png
In the old days Merge would merge all like colors that are visible and delete anything behind them. Now it divides and leave colors behind so there's a ton of extra, useless, objects left behind that get in the way when I'm forced to unite the mess together manually afterwards.
But even with simple blocks of color, not that many points, no groups, and a mere 15 objects merge won't work.
If anyone has any solutions to this you'd earn my undying gratitude.
The objects had the Overprint attribute checked in Attributes panel. With this option on Illustrator leaves fragments unmerged to match the assumed intention behind having Overprint one. This is a normal expected behaviour, but not a transparent one.
If you have this problem, don’t hesitate to leave the comment to force the team to rethink the UX behind this.
Glad that I found this post because I was tearing my hair out for half an hour with the same issue. It is completely confusing to have the program behave this way when you normally don't work with the overprint feature. I normally never have the attributes window, and don't expect a tool to behave different than it's standard definition. Merge should mean to merge objects - not slice and divide them. This is a very confusing interaction and makes it seem like a bug or an error in the program and not an "expected behavior". Please consider a notification in the pathfinder window to display a message of "Overprint Enabled In Attribute Window" If the merge button is clicked while overprint is enabled as this at least will be a clue that something is out of the ordinary.
Aaron Rivera commented
FYI, it turns out the objects were set to Overprint, so I had to expand the objects, select them, then go into the attributes panel to turn off Overprinting.
Thanks to Monika Gause at the Adobe forums for the fix.