I have the same problem for 1 repo (others work)

Jenkins 2.232
git 4.2.2
git-client 3.2.1
git-server 1.9
github 1.29.5
github-api 1.111
github-branch-source 2.6.0
github-organization-folder 1.6

 ERROR: [Fri Apr 17 15:03:39 PDT 2020] Could not fetch sources from navigator org.jenkinsci.plugins.github_branch_source.GitHubSCMNavigator@21f39e43
com.fasterxml.jackson.core.JsonParseException: Unexpected character ('<' (code 60)): expected a valid value (JSON String, Number, Array, Object or token 'null', 'true' or 'false')
at [Source: (StringReader); line: 1, column: 2]
at com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1840)
at com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:712)
at com.fasterxml.jackson.core.base.ParserMinimalBase._reportUnexpectedChar(ParserMinimalBase.java:637)
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1916)
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:772)
at com.fasterxml.jackson.databind.ObjectReader._initForReading(ObjectReader.java:357)
at com.fasterxml.jackson.databind.ObjectReader._bindAndClose(ObjectReader.java:1704)
at com.fasterxml.jackson.databind.ObjectReader.readValue(ObjectReader.java:1261)
at org.kohsuke.github.GitHubResponse.parseBody(GitHubResponse.java:85)
at org.kohsuke.github.GitHubPageIterator.lambda$fetch$0(GitHubPageIterator.java:145)
at org.kohsuke.github.GitHubClient.createResponse(GitHubClient.java:406)
at org.kohsuke.github.GitHubClient.sendRequest(GitHubClient.java:360)
Caused: org.kohsuke.github.HttpException: Server returned HTTP response code: 200, message: '304 Not Modified' for URL: https://github.xxx/api/v3/repos/xxx/contents/?ref=refs%2Fheads%2Fmaster
at org.kohsuke.github.GitHubClient.interpretApiError(GitHubClient.java:445)

 Edit: 

I tried this but no luck https://superuser.com/questions/1459241/jenkins-and-github-enterprise-2-17-failing-pull-request-builds-only

I made a commit on the repo (just changed a readme file) and it re-scanned and it worked. 

Mike Erickson sean qian
So, this is an intermittent failure? 

Could one of you file this as an issue for that github-api library (https://github.com/github-api/github-api) .  It is something that will need to be worked on there. 

I think I found the source of this problem.

There is bug in Push event payloads that returns the wrong url.
All other occurrences of "url" take the form "https://api.github.com/repos/[fullName]".
For Push event repository records, they take the form "https://github.com/[fullName]".

https://github.com/hub4j/github-api/blob/66f22de90fd0d53de4d9e79b8fa202fb0af8310f/src/main/java/org/kohsuke/github/GHRepository.java#L2842-L2853

This is consistent with this issue not reproducing when scanning.

Fix should be in the next version of the github-api.