I've occasionally run into issues with the tests Driver/linker.swift, Driver/linker-clang_rt.swift and Driver/embed-bitcode.swift being flaky.
The following test results are with e052da7d8886fa0439677852e8f7830b20c2e1da (tag: swift-DEVELOPMENT-SNAPSHOT-2019-09-25-a) but I've seen the same issues at other points as well.
Here's a Python runner to check this:
Running the script once gave me 4 failures out of 200 runs.
N.B. The script also runs 4 other tests, not sure how those are interacting with the flaky tests, but it seems hard/impossible to get the failure if only the 2 flaky tests are run.