A "cliche" is kind of like a "stereotype," however it refers to an overused idea/topic of conversation/some other thing. It is so commonly discussed, known, or used that it is no longer effective or interesting, and is often annoying.
In this situation, there is the stereotype: "Japan is the land of geisha, manga, and other weird things." This topic has been emphasized so much despite being largely untrue, so a Japanese person starting a conversation with a Westerner might consider it "cliche" if the first thing they are asked about Japan is in regard to geishas or manga, even though those things are not common in their everyday lives.
Consider another example. A Western guy goes to a ramen restaurant with his Japanese friend in Japan. When they get their ramen the Western guy picks up his chopsticks and starts eating his food with ease. His friend gasps in surprise and starts saying, "Wow! You use chopsticks SO WELL!" This Western guy has probably heard this sentence dozens of times since he arrived in Japan, to the point where he can EXPECT a Japanese person to say it whenever he touches chopsticks. Rather than a compliment, it seems that they were all expecting him to be completely inept at using a simple eating utensil. It has become an irritating "cliche" that he can expect to hear over and over again whenever he goes out to eat with a Japanese friend.