This bug is straightforward. When a checkbox is neither true nor false, the items are sorted inconsistently. I believe they are currently being sorted by the file name.
Please check the image attached.. it’s everything there.
Does anyone know a workaround for this issue?
Hello Cyprian,
It is currently intentional to interpret “indeterminate” as “false” for sorting purposes.
Please, open a Feature Request for this.
Also, please follow the BR template next time you open a Bug Report. Thanks!
Could you at least provide your debug info 
…
I don’t really seem to be able to repro in the Sandbox vault + MacOS Sequoia + Obsidian 1.12.7 (app + installer)
E.g.: check sorted by A > Z
and check sorted by Z > A
You could try to use a formula (potentially) and sort your base using that formula instead 
(The formula field can be hidden)
E.g.: As you can coerce boolean values into numbers using one or another function:
number(check)
or
check.isTruthy()
… which converts false to 0 and true to 1 and doesn’t seem to output anything for the null/“indeterminate” value (for notes where check exists as a key but holds neither true nor false), leaving these at the bottom (whether I sort by the Untitled formula by 0 > 1 or 1 to 0)
Or, depending if you want to see the null/“indeterminate” value appearing at the top, something like this could be another possibility:
if(check.isType("null"), 0, number(check) + 1)