Nothing impolite about it. Might well be a regional British expression

Come again doesn't have an impolite touch, unless that is made by the way you say it, but normally not. It isn't that common these days, at least not with younger people and would be considered fairly informal. That's my opinion at any rate ;-). BTW just as a helpful comment, I would say "recently" rather than "currently", as you can't really combine "currently" (i.e. now) with the past.

My Partner is from Yorkshire and uses it so it might indeed by regional only.

I just found a site phrased like this: "Computer Stupidities. Come Again?
Sometimes, especially when conversing on the phone, people misunderstand each other. Sometimes it's funny. Sometimes it's frustrating." (The other references I found were either born-again Christian in nature - or relating to multiple orgasms.) Yes it's informal but not rude, perhaps more typical of older generations - but I also know it from the States.

I know it from the south of England, and my wife is from Lancashire - two parts of England both physically and mentally separated - so it seems a fairly generally spread expression in England.

very common in the US, too - but I hear it mostly used, when someone wants the other person to repeat a somewhat uncommon, weird or outrageous statement

From Stephen Fry, "Making History" (quoted from memory):
- "Put that down! That's a male sterilisation pill!"
- "Come again?"
- "...is exactly what you won't, if you don't put that down!"

exactly

Another Stephen Fry quote he used it in "Absolute Power" First time I heard it. He used it in the "Ich glaube ich hoere nicht recht" way