I'm having the same issue, although I'm using Unity 5.3.4f1. Asset Bundles containing built-in Unity assets (e.g., prefabs, materials, etc.) build just fine, but when I try to add any of my Spine prefabs to an asset bundle, Unity crashes abruptly.
Like the thread's author, I can manually set each Spine prefab's Skeleton Mesh Mesh Filter to have a Mesh of "None", which allows me to build some of my prefabs, but some cause Unity to either hang (requiring a force quit), or crash, seemingly at random.
I've attached an editor log with the stack trace at the end of the file, as well as screenshots of a Spine prefab with its attached components.
Any ideas?
I tried to edit my reply to include another attachment, but the forum software just kept refreshing the page without the attachment posted. Now that I think about it, it might be because the attachment was too large. Either way, I've created a Unity project that shows the issue at hand:
https://dl.dropboxusercontent.com/u/143283/asset-bundle-crash-project.zip
There is a single prefab, "avatar_boy," created from a skeleton with 5 materials. I've added a Unity Editor menu item called "Build Asset Bundles" under the "Assets" menu header. When this is selected, Unity crashes.
Here are my steps:
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Drag these files into the Unity Editor: avatar_boy.json, avatar_boy.atlas.txt, avatar_boy.png, avatar_boy2.png, avatar_boy3.png, avatar_boy4.png, and avatar_boy5.png
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Right-click the newly created "avatar_boy_SkeletonData" object in the Project window and select Spine -> Instantiate (SkeletonAnimation)
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Drag the created "avatar_boy" game object from the Hierarchy window into the Project window to create a prefab
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Add the "avatar_boy" prefab to a new "character" asset bundle
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Select Assets -> Build Asset Bundles
At that point, Unity crashes.
I wanted to give another update on this. I submitted a bug report to Unity (here: https://fogbugz.unity3d.com/default.asp?783953_gsjl4vqqtmlpg43r), and they're taking a look at the crash. They did mention that Esoteric should also look into why its assets are causing Unity to crash, when "standard" Unity assets do not. I'm hopeful both Unity and Esoteric can come up with fixes on both sides.
Another thing to note is that downloading the project I'd linked to in my Dropbox account, you might not be able to reproduce the issue on first try. However, if, after you build the asset bundles for the project, you then change the asset bundle containing avatar_boy to another bundle (e.g., put it in a new asset bundle called, "test") and build the asset bundles, the project should crash.
I hope this helps you zero-in on the issue.