I noticed several times that I took damage between entering a nether portal and coming out on the other side. When testing, I took 1 heart the first time, 1/2 heart the second and 1 the third. This only happened coming to the overworld from the nether. I heard the cracking sound of damage taken while the computer was on the 'downloading terrain' screen.
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I searched for 'portals' in the comments. Your search functions aren't very well set up. If you made it easier to search for issues, you'd get a lot fewer duplicates.
Duplicate of MC-793 - If you have not, please use the search function in the future, to see if your bug has already been submitted. If you could not find the original report, please comment with the keywords you searched for.