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.
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
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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