You might be missing an index. See Query engine.
You are accessing a Session instance concurrently from multiple threads. Session instances are not thread safe. Enabling DEBUG logging for SessionDelegate provides stack traces for both sessions involved. Note: this should be used for debugging only as it has a major impact on system performance.
You need to setup a regular job for compacting the segments.
Debugging merge conflict errors is now possible by enabling DEBUG logs on org.apache.jackrabbit.oak.plugins.commit.MergingNodeStateDiff and org.apache.jackrabbit.oak.plugins.commit.ConflictValidator. This option is available via OAK-3057 since Oak 1.0.17, 1.2.3, 1.3.3.