[Bug Report] Getting "There were stale violations found, please run `packwerk update-todo`" even there is no stale violations

Description
I'm getting "There were stale violations found, please run packwerk update-todo" when I run check command againts some files.
For this you have to have one violation in several files.

For example:

# This file contains a list of dependencies that are not part of the long term plan for the
# 'packs/one' package.
# We should generally work to reduce this list over time.
#
# You can regenerate this file using the following command:
#
# bin/packwerk update-todo
---
".":
  "::ApplicationController":
    violations:
    - dependency
    files:
    - packs/one/bar.rb
    - packs/one/baz.rb

To Reproduce

1. Create a dependency violation in the first file.
2. Create the same dependency violation in another file within the same package.
3. Run packwerk update-todo in order to generate package_todo.yml file.
4. Run packwerk check path/to/the/first_file.rb.

Actual Behaviour

• Command returns 1 status.
• Command output contains info about stale violations.

📦 Finished in X.XX seconds

No offenses detected
There were stale violations found, please run `packwerk update-todo`

Expected Behaviour

• Command returns 0 status
• Command output has no info about stale violations

Version Information

• Packwerk: 3.1.0
• Ruby: 3.2.1

Additional Context
3.0.1 has no this problem

Reproduce the issue using packwerk update-todo and packwerk check path/to/the/first_file.rb with the same violation in multiple files. Compare the behavior with Packwerk 3.0.1 and 3.1.0, then verify that the targeted check returns status 0 without stale-violation output.