cli: bun --bun run <script> sometimes does not look for scripts

[DonIsaac]

What version of Bun is running?

1.1.44-canary.74+68089a099

What platform is your computer?

Darwin 24.1.0 arm64 arm

What steps can reproduce the bug?

git clone [email protected]:expressjs/express
cd express
bun install
bun --bun run test

What is the expected behavior?

Tests run

What do you see instead?

error: Module not found '<omitted>/express/test'

Bun v1.1.44-canary.74+68089a099 (macOS arm64)

Additional information

• bun run test works fine
• I cannot repro on a newly initialized codebase. Steps I took
  • bun init
  • add this script: "test": "bun index.ts" -- works
  • then installing typescript and trying "test": "tsc --noEmit" -- also works
• adding/removing tsconfig.json has no effect

[nektro]

will be fixed by #15117