Pages deployment not running `npm run buld`

We had a dead production deployment go out this morning for a Pages project linked to a Github repo. There was a merge to the 'prod' branch which triggered a deployment but Cloudflare's build step did not run
npm run build
so the /functions folder was not generated and it just deployed nothing. To make things interesting, we had the exact same commit trigger a Preview deployment on our
dev
branch without any issues.

The log from the broken production deployment (no functions deployed):
05:33:00.314    A wrangler.toml file was found but it does not appear to be valid. Did you mean to use wrangler.toml to configure Pages? If so, then make sure the file is valid and contains the `pages_build_output_dir` property. Skipping file and continuing.
05:33:01.587    Finished
05:33:01.588    Note: No functions dir at /functions found. Skipping.


The logs from the successful preview deployment of THE SAME COMMIT:

08:13:02.693    Checking for configuration in a wrangler.toml configuration file (BETA)
08:13:02.694    
08:13:02.694    Found wrangler.toml file. Reading build configuration...
08:13:02.816    A wrangler.toml file was found but it does not appear to be valid. Did you mean to use wrangler.toml to configure Pages? If so, then make sure the file is valid and contains the `pages_build_output_dir` property. Skipping file and continuing.
08:13:04.086    Detected the following tools from environment: nodejs@20.11.0, npm@9.6.7
......
Installs node, running npm install etc--
......
08:13:48.027    Found Functions directory at /functions. Uploading.
08:13:49.620    ✨ Compiled Worker successfully


there is an issue with the wrangler.toml but that happened in both successful builds and non building deployments. Any ideas what's going on?
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