AssertionError: Internal error: method must be called on parsed file only

Bug Report

When I run mypy==0.991 in parallel, the following error randomly happens.

Traceback (most recent call last):
  File "/home/my_name/.pyenv/versions/3.9.16/bin/mypy", line 8, in <module>
    sys.exit(console_entry())
  File "/home/my_name/.pyenv/versions/3.9.16/lib/python3.9/site-packages/mypy/__main__.py", line 15, in console_entry
    main()
  File "mypy/main.py", line 95, in main
  File "mypy/main.py", line 174, in run_build
  File "mypy/build.py", line 193, in build
  File "mypy/build.py", line 276, in _build
  File "mypy/build.py", line 2903, in dispatch
  File "mypy/build.py", line 3284, in process_graph
  File "mypy/build.py", line 3365, in process_fresh_modules
  File "mypy/build.py", line 2109, in fix_cross_refs
AssertionError: Internal error: method must be called on parsed file only

To Reproduce

I cannot identify to reproduce this problem because this error randomly happens (2-3% probabiliy), but I observed this problem only when I ran mypy in parallel on multiple files.

Your Environment

• Mypy version used: mypy==0.991
• Mypy command-line flags: mypy --follow-imports silent --config-file pyproject.toml path/to/foo.py
• Mypy configuration options from mypy.ini (and other config files): pyproject.toml

[tool.mypy]
ignore_missing_imports = true
[[tool.mypy.overrides]]
module = "third_party.*"
ignore_errors = true
[[tool.mypy.overrides]]
module = "requests.*"
ignore_missing_imports = true

• Python version used:3.9.16

Start in mypy/build.py at process_fresh_modules, fix_cross_refs, and the surrounding dispatch and process_graph calls shown in the traceback. Run the reported mypy==0.991 command concurrently on multiple files, focusing on the intermittent parallel failure. Done means the assertion no longer occurs during parallel runs and the regression is covered by a reproducible test.