Why did the science experiment break up with the other experiment?

This joke gets its chuckle from some clever wordplay, specifically a pun on the word "chemistry." The humor mechanism relies on the audience understanding that "chemistry" can refer both to the scientific field of study, which is directly relevant to a "science experiment," and also to the less tangible, but very real, spark or connection between two people in a relationship.

When we talk about people "having chemistry," we mean they get along well, have a good rapport, or feel a mutual attraction. This is the human relationship context. On the other hand, science experiments often literally involve the principles of chemistry, like mixing substances or observing reactions. The joke's brilliance lies in taking this scientific concept and applying it to a human relationship scenario, creating an amusing clash of literal and figurative meanings that suggests a lack of compatibility.