I have the same issue since upgrading to el Capitan. Notes will open and seem like it might work but then it crashes within a few seconds.
Here's my crash report
Process: eclipse [28373]
Path: /Applications/IBM Notes.app/Contents/MacOS/rcp/eclipse/plugins/com.ibm.rcp.base_9.0.1.20131002-14 04/macosx/x86/eclipse
Identifier: com.ibm.Notes
Version: 9.0.1 (13287)
Code Type: X86 (Native)
Parent Process: ??? [1]
Responsible: eclipse [28373]
User ID: 501
Date/Time: 2016-01-08 07:32:52.687 -0800
OS Version: Mac OS X 10.11.2 (15C50)
Report Version: 11
Anonymous UUID: 978E8096-EA7D-F327-2592-4F6459703AF3
Time Awake Since Boot: 1500000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_PROTECTION_FAILURE at 0x00000000bf800ffc
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0xbf800ffc:
Stack Guard 00000000bc000000-00000000bf800000 [ 56.0M] ---/rwx SM=NUL
--> Stack Guard 00000000bf800000-00000000bf801000 [ 4K] ---/rwx SM=COW
Stack 00000000bf801000-00000000c0000000 [ 8188K] rw-/rwx SM=COW
Application Specific Information:
Java information:
Exception type: Bus Error (0xa) at pc=000000009e7ddf97
Java VM: Java HotSpot(TM) Client VM (20.65-b04-468 mixed mode macosx-x86)
Current thread (0000000006801000): JavaThread "main" [_thread_in_native, id=-1555845120, stack(00000000bf800000,00000000c0000000)]
Stack: [00000000bf800000,00000000c0000000]
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j com.ibm.workplace.noteswc.macosx.NotesBootstrapMac.SetParent(II)I+0
j com.ibm.workplace.noteswc.macosx.NotesBootstrapMac.setParent(II)I+2
j com.ibm.workplace.noteswc.swt.NotesControl.setHandleNative(I)V+37
j com.ibm.workplace.noteswc.swt.NotesControl$1$1.controlledRunInUIThread(Lorg/ecl ipse/core/runtime/IProgressMonitor;)Lorg/eclipse/core/runtime/IStatus;+59
j com.ibm.workplace.noteswc.NotesWcDefaultUIJob.runInUIThread(Lorg/eclipse/core/r untime/IProgressMonitor;)Lorg/eclipse/core/runtime/IStatus;+49
j org.eclipse.ui.progress.UIJob$1.run()V+51
j org.eclipse.swt.widgets.RunnableLock.run()V+11
j org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Z)Z+29
j org.eclipse.swt.widgets.Display.runAsyncMessages(Z)Z+5
j org.eclipse.swt.widgets.Display.readAndDispatch()Z+143
j org.eclipse.ui.internal.Workbench.runEventLoop(Lorg/eclipse/jface/window/Window $IExceptionHandler;Lorg/eclipse/swt/widgets/Display;)V+9
j org.eclipse.ui.internal.Workbench.runUI()I+393
j org.eclipse.ui.internal.Workbench.access$4(Lorg/eclipse/ui/internal/Workbench;) I+1
j org.eclipse.ui.internal.Workbench$5.run()V+23
j org.eclipse.core.databinding.observable.Realm.runWithDefault(Lorg/eclipse/core/ databinding/observable/Realm;Ljava/lang/Runnable;)V+12
j org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Lorg/eclipse/swt/widget s/Display;Lorg/eclipse/ui/application/WorkbenchAdvisor;)I+18
j org.eclipse.ui.PlatformUI.createAndRunWorkbench(Lorg/eclipse/swt/widgets/Displa y;Lorg/eclipse/ui/application/WorkbenchAdvisor;)I+2
j com.ibm.rcp.personality.framework.internal.RCPApplication.run(Ljava/lang/Object ;)Ljava/lang/Object;+108
v ~StubRoutines::call_stub
j sun.reflect.NativeMethodAccessorImpl.invoke0(Ljava/lang/reflect/Method;Ljava/la ng/Object;[Ljava/lang/Object;)Ljava/lang/Object;+0
j sun.reflect.NativeMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Objec t;)Ljava/lang/Object;+87
j sun.reflect.DelegatingMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/O bject;)Ljava/lang/Object;+6
j java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lan g/Object;+161
j org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(Lj ava/lang/Object;Ljava/lang/String;[Ljava/lang/Class;[Ljava/lang/Object;)Ljava/la ng/Object;+15
j org.eclipse.equinox.internal.app.EclipseAppHandle.run(Ljava/lang/Object;)Ljava/ lang/Object;+196
j org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(Lja va/lang/Object;)Ljava/lang/Object;+103
j org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(Ljava/lang/O bject;)Ljava/lang/Object;+29
j org.eclipse.core.runtime.adaptor.EclipseStarter.run(Ljava/lang/Object;)Ljava/la ng/Object;+149
j org.eclipse.core.runtime.adaptor.EclipseStarter.run([Ljava/lang/String;Ljava/la ng/Runnable;)Ljava/lang/Object;+66
v ~StubRoutines::call_stub
j sun.reflect.NativeMethodAccessorImpl.invoke0(Ljava/lang/reflect/Method;Ljava/la ng/Object;[Ljava/lang/Object;)Ljava/lang/Object;+0
j sun.reflect.NativeMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Objec t;)Ljava/lang/Object;+87
j sun.reflect.DelegatingMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/O bject;)Ljava/lang/Object;+6
j java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lan g/Object;+161
j org.eclipse.equinox.launcher.Main.invokeFramework([Ljava/lang/String;[Ljava/net /URL;)V+211
j org.eclipse.equinox.launcher.Main.basicRun([Ljava/lang/String;)V+126
j org.eclipse.equinox.launcher.Main.run([Ljava/lang/String;)I+4
j com.ibm.rcp.core.internal.launcher.Main.startLaunch([Ljava/lang/String;)V+227
j com.ibm.rcp.core.internal.launcher.Main.main([Ljava/lang/String;)V+262
j com.ibm.rcp.core.internal.launcher.Main.run([Ljava/lang/String;)I+1
v ~StubRoutines::call_stub