the same happened to me in 1.9.4 vanilla with an iron golem in std 2x3 portal. when you follow your critter through the portal you probably push its hitbox into obsidian
the seed is 1435720922980048131; it's maybe 1.7 created, issues only appeared after the recent changes to 1.9.* i just sorted that with the proper egg used on the spawner.
the steps were quite simple. you update to 1.9 walk through your nether portal towards your blaze grinder and you find it grinding nothing with a pig spawner sitting in the center.
as of vanilla 1.9.2 automated update, horses nor golems travel full blocks up. problem persists.
confirmed for the 1.9 as downloaded today (02Mar). horses going through portal receive suffocation damage from the portal frames for the most part. i had this problem in both overworld and nether.
[1.9 vanilla] neither do Iron Golems on the leash. Cows, cats, dogs climb 1 block tall inclines fine.
i have encountered this for a few times in last two weeks, which is -Vanilla 1.11.2. The troublesome partial? download of new launcher had 38.80MB and ended with the same error message. Well, i took the .tmp launcher file from the tmp directory and replaced the the old launcher in minecraft directory with it. then, another download happened of 3.89MB and now the launcher says it's version 1.6.76 and appears to be running fine.
nota bene - i've encountered this issue even when installing the brand new minecraft after removing all the old (supposedly corrupted) files. as it goes, it appears to me to be a mere pathfinding glitch of some kind of batch file or maybe it's firewall related (different rights granted to the file manager as opposed to the petty minecraft updater).