Here’s a partial list of known issues for Aperture in El Capitan from this an old discussion forum link 
- The thumbnails in list view are upside down. (Apple has been intermittently screwing up EXIF orientation tags since iPhoto 5.)
- If you add a Curves adjustment the straighten adjustment will not be visible in the exported images. The exported images won’t show straightening. (This is unpredictable behavior.)
- When brushing adjustments, the position can be slightly off, one pixel or so.
- The link to the plug-in page no longer works in the Aperture menu (this is Yosemite too)
- You can no longer order print products from Aperture (Yosemite too)
- Soft proofing is broken
- When exiting app the progress window that’s displayed has no content
The levels/straighten export bug is the worst I’ve read about.
Except for what happened today. Aperture opened, but the workspace was somewhere else in space. It acted like it was off-monitor somewhere. Aperture worked normally in a different user account, so I figured it was something about my account. Removing preferences didn’t help.
I changed Mission Control so that Dashboard was no longer a space — and Aperture’s workspace returned. But reenabling Dashboard space didn’t affect Aperture.
Someone noticed in El Capitan beta that the workspace might vanish. In which case clicking on the Aperture icon in the Dock would restore it. If it happens again I’ll try that, and also the Aperture context menu Windows item.
 Apple’s new Discussion Forum software is amazingly broken. They really can’t do anything right any more. Fortunately I’d Pinboarded that link.
PS. Aperture has more trouble with El Capitan than most older software. Perhaps it’s more dependent on undocumented features than other software, or perhaps the code base is unusually problematic.
Update 7/24/2016: I’ve just seen iTunes lose its workspace. El Capitan really doesn’t want Dashboard to be a space. At least not the way I have Mission Control setup. I made it an overlay.
Update 9/22/2016: Apparently if you apply AutoEnhance first you can avoid the levels/straighten bug.
Update 9/28/2016: Aperture is being tested in Sierra. It works well for relatively modern hardware, so there’s cautious optimism for good support by the .2 release (Feb 2017?). It crashes badly with older Sierra-supported Macs. freediverx01 reported on the status of known El Cap bugs in Sierra
- Thumbnail are upside-down in list view
- With a Curve adjustment and then a straighten adjustment - the exported image is OK
- Brush adjustments - seem OK - no offset
- Link to Plug-in menu is OK - I used BorderFX as a test
- Soft Proofing does not work
- Full Screen (f) is OK - does not freeze Aperture