When someone puts a flea in your ear, it can mean a variety of things, depending on where you live. English speakers differ on the precise meaning of this phrase, and there are numerous versions in other languages that are also quite diverse. The origins of the term are fairly clear, but the confusion over the meaning seems to have emerged almost as soon as the phrase did.
This term does not reference literally sticking a bug into someone's ear, but it does make a reference to a problem that was pretty common in the Middle Ages: being infested with fleas, body lice, and other parasites. Many people struggled to control parasite populations in their homes and communities, and getting a flea in the ear would have been extremely annoying, since the creature would have presumably scrabbled around and possibly bitten the person, causing pain and irritation.
The first reference to putting a flea in someone's ear is in French literature from the 14th century. In the original sense, the term was used to describe the practice of provoking desire in someone else. In a rather lewd French poem, the poet writes about putting a flea in a young woman's ear in the sense of causing her to become intoxicated with desire. The Dutch used this phrase in the sense of being restless or edgy, presumably because one would be understandably twitchy about a flea in the ear canal.
English authors first encountered the term in translation, and they were apparently uncertain about what it meant. Over time, the phrase came to be used in reference to planting suspicions or ideas in someone's mind that could not be ignored. Much like the theoretical flea, these ideas would buzz and nibble away at the host, forcing him or her to deal with them. The French still refer to “putting a flea in your ear” in this sense, apparently having abandoned the romantic usage of the term.
Americans have come up with a unique twist on the phrase that has nothing to do with any of the above. They usually use the term to refer to rebuking or punishing someone, as in “I sent him away with a flea in his ear.” Presumably, this refers to the torment of having a bloodsucking insect in your ear, but it can be rather confusing to people who use the idiom to talk about planting suspicions.