Unfortunately there is no real fix for your issue, as this seems to be expected behavior of uMatrix. This is because the PDF's are mostly on a different domain than the site you are currently on and would be downloaded without the domain being open in a tab.
There are a few issues on github regarding this issue, you can find them here and here.
While there is not a real "fix" to this behavior, there are a few workarounds which I will list here to make it easy for you to pick one which fits your workflow.
Workarounds
1. Changing default action for PDF's
You can change the behavior of chromium to download PDF's on left-click instead of opening them in the browser. This is by far the most comfortable of the workarounds, but may be annoying if you often look at PDF's directly in the browser.
- Open the chromium settings
- Click on Privacy and Security
- Click on Site Settings
- expand Aditional Content Settings
- click PDF-Documents
- Select
Download PDF's
instead of open PDF's in Chromium
While my chromiums menu is in german, the symbols and placement, as well as my english translation should give enought clues to find the buttons with ease.
2. download PDF via button in chromiums PDF viewer
You could download the files via a button in the integrated PDF viewer:
If you don't want to disrupt the progress of the site you are currently browsing, you can simply open the link in a new tab with your middle mouse button, or Ctrl + left-click.
3. change uMatrix settings for "Others"
I suspect that most people won't download PDF's from mostly the same sites, therefore this solution could be the most timeconsuming solution.
Depending on the link, it could also be annoying to find the domain the PDF is hosted on.
- Click on the uMatrix Plugin in the top right corner of chromium's menubar
- For the PDF's domain, select allow in "Others" tab on the right side
- right-click on the link and select save as
Note that these instructions are tested and worked on my system with Arch and Chromium 98.0.4758.102