this only happens when updating from a version pre-3.0.2 (maybe transiently, if you updated 3.0.1 > (ok) > 3.0.2 > (crash) > 3.5).
some more detailed explanation: 3.0.1 had a nodetype definition of the expression node in place that sais "metaData is mandatory" (see owfe-nodetypes.xml in workflow module). This nodetype definition is copied to the repositories/magnolia/repository/nodetypes/custom_nodetypes.xml file when installing 3.0.1. When updating this instance to 3.5 (by either replacing jars or copying the repository to a newly created instance) an update task of 3.5 removes the metadata node. Since you then still have the original custom_nodetypes.xml file in place Jackrabbit complains with the exception above.
As mentioned before, fix this by adjusting the appropriate expression nodetype in custom_nodetypes.xml or just replace the whole file with the one attached entirely.
To fix that you have to replace the file repositories/magnolia/repository/nodetypes/custom_nodetypes.xml before you start updating with the one of 3.5