I have been researching this issue for few days without luck. I found many posts reporting similar issues but not with Gerrit code review.
The case is that we have a repo which contains many branches. Only one branch (dev) show this problem.
org.eclipse.jgit.errors.MissingObjectException: Missing unknown 5f3190e131541cec4ef7176262eaf4a03c4a4e6c
        at com.google.gerrit.server.git.MergeOp.integrateIntoHistory(MergeOp.java:497)
        at com.google.gerrit.server.git.MergeOp.merge(MergeOp.java:433)
        at com.google.gerrit.server.change.Submit.apply(Submit.java:225)
        at com.google.gerrit.server.change.Submit.apply(Submit.java:83)
        at com.google.gerrit.httpd.restapi.RestApiServlet.service(RestApiServlet.java:341)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
        at com.google.inject.servlet.ServletDefinition.doServiceImpl(ServletDefinition.java:286)
        at com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:276)
        at com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:181)
        at com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:91)
To reproduce the error just do a change. Commit and push to gerrit refs/for/dev. Once I click on Submit in Gerrit I get the above error.
The revisions on the server are as follows:
- Gerrit Code Review (2.13.1)
 - Git-2.1.0
 - Java 1.7.0_71
 
Running git fsck on the server side return Ok. 
Running git show 5f3190e131541cec4ef7176262eaf4a03c4a4e6c returns
fatal: bad object 5f3190e131541cec4ef7176262eaf4a03c4a4e6c
Changing the project preference in Gerrit from Merge if necessary to Rebase if necessary got this exception.
Caused by: com.google.gerrit.server.git.UpdateException: org.eclipse.jgit.errors.MissingObjectException: Missing unknown 5f3190e131541cec4ef7176262eaf4a03c4a4e6c
        at com.google.gerrit.server.git.BatchUpdate.executeUpdateRepo(BatchUpdate.java:673)
        at com.google.gerrit.server.git.BatchUpdate.execute(BatchUpdate.java:400)
        at com.google.gerrit.server.git.MergeOp.integrateIntoHistory(MergeOp.java:478)
        ... 43 more
Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing unknown 5f3190e131541cec4ef7176262eaf4a03c4a4e6c
        at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:158)
        at org.eclipse.jgit.lib.ObjectReader.open(ObjectReader.java:227)
        at org.eclipse.jgit.revwalk.RevWalk.parseAny(RevWalk.java:859)
        at org.eclipse.jgit.revwalk.RevWalk.parseCommit(RevWalk.java:772)
        at com.google.gerrit.server.git.CodeReviewCommit$CodeReviewRevWalk.parseCommit(CodeReviewCommit.java:110)
        at com.google.gerrit.server.git.SubmoduleOp.updateSubmodule(SubmoduleOp.java:461)
        at com.google.gerrit.server.git.SubmoduleOp.composeGitlinksCommit(SubmoduleOp.java:369)
        at com.google.gerrit.server.git.SubmoduleOp$GitlinkOp.updateRepo(SubmoduleOp.java:85)
        at com.google.gerrit.server.git.BatchUpdate.executeUpdateRepo(BatchUpdate.java:661)
        ... 45 more
It is worth mentioning that the hash 5f3190e131541cec4ef7176262eaf4a03c4a4e6c does not show anywhere on the Gerrit code review page (only in the error message). Any new commit will cause this error.