MongoVersionGCSupport uses the default batchSize when it queries for possibly deleted documents. The default will initially read 100 documents and then as many as fit into a 4MB response. Depending on the document size a couple of thousand will fit in there and take time to process. It may happen that the MongoDB cursor then times out and the VersionGC fails.
An easy and safe solution is to reduce the batch size to a given number of documents.