We updated the plugins we have to the latest version.
After restart 11 plugins failed to load.
First we did not notice untill we noticed some builds were giving strange issues.

We checked the plugin list.
The failing plugins were listed in 'available' list instead of 'installed' list.

Looking in the catalina log file we finally noticed the cause of it:

Some were reporting a dependency missing, which was not reported in the update UI.
SEVERE: Failed Loading plugin findbugs
java.io.IOException: Dependency analysis-core (1.0) doesn't exist
at hudson.ClassicPluginStrategy.loadPluginDependencies(ClassicPluginStrategy.java:374)
at hudson.ClassicPluginStrategy.load(ClassicPluginStrategy.java:237)
at hudson.PluginManager$1$3$2$1.run(PluginManager.java:202)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:146)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:259)
at hudson.model.Hudson$3.runTask(Hudson.java:642)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:187)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:94)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:619)

Some were giving even worse errors:
SEVERE: Failed Loading plugin testabilityexplorer
hudson.util.IOException2: Failed to initialize
at hudson.ClassicPluginStrategy.load(ClassicPluginStrategy.java:278)
at hudson.PluginManager$1$3$2$1.run(PluginManager.java:202)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:146)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:259)
at hudson.model.Hudson$3.runTask(Hudson.java:642)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:187)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:94)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.NoClassDefFoundError: hudson/plugins/analysis/core/HealthAwarePublisher
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
at java.net.URLClassLoader.access$000(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195)

So all the plugins which failed to load are dependent on a new plugin. During upgrade this was not reported.
To support this successful the new dependency should be listed in the update list for plugins as well.