A few thoughts:
1) I don't know about allergies...that may be it, but I kinda doubt it.
2) When racking beer, I always taste some. It almost always has some yeast and such swirled into it at that point. Often, it makes my throat scratchy, and is fairly harsh. It always goes away once the beer finishes and settles. Maybe there are compunds in the yeast cake that do this. I know the yeast cake tastes harshly bitter sometimes, so maybe it's hop components.
3) There's nothing in there that will kill you or hurt you even if you have an infection. Let it finish and taste it and don't be afraid (unless you have severe allergies or something Fortunately, beer can't grow salmonella or the like.
4) A cool and cleaner way to rack is this: Fill your racking cane with iodophor solution. You can shove the cane into the other end of the hose so it's a loop until you need it and throw the whole loop into a bucket of sanitizer. When you want to rack, pull the cane out of the hose and hold both ends upward and at even levels so the cane and hose stay completely full. In one smooth motion, shove the cane in the beer to be racked and lower the other end of the hose (I put my thumb over that end as I'm doing this, but I sanitize my thumb ). The sanitizer in the hose will flow downhill and start the siphon. Collect the first few ounces of sanitizer in some container and then switch the hose over to wherever you're racking to once it's just beer coming out. It's really easy and very sanitary.