Is it bad to make a joke during a presentation ? I am a PhD student in economics and working on stuff like Hopf bifurcations and limit cycles used often in mathematics. 

One of the graphics that I will use for my presentation is very similar to one of the photos in album booklet (dark side of the moon) of the legendary progressive rock band Pink Floyd. Here is the link ;

Album cover

It is like a limit cycle (it is a heartbeat sequence, note that there are also bifurcation analysis for heartbeats) and gives a quick idea about the concept. 

I am wondering if it is really appropriate to make this kind quick jokes during presentations. Anybody having bad experiences about that ?
I would encourage you not to force humor into - or out of - a presentation, depending on your goals for the presentation and the context of the situation you are in.

The thing with humor is it is deeply contextual, and how it is received depends heavily on the delivery, the audience, and how you are perceived as the 'performer'. For a Brilliant, Serious Scholar, a light-hearted joke can help to improve your likability and make the talk more memorable and understandable to a wider audience. On the other hand, a Mewling Youngling cracking wise can bring about eye rolls and grumbling and help to cement an impression that you are insufficiently serious, plugging your talk with frippery because you don't have anything really substantive to add. 

It's annoying - and often unfair - that two people can say the same thing and have the reception of the statement be completely and utterly different, but in practice that's how it goes.

Your talk is your performance, your work, and you decide what impression you want to give, how you present yourself, and how you want people to view you. Humor can be a useful part of that, neutral, or counter-productive. 

Personally, as a one-size-fits-all suggestion, if you plan a joke I suggest you also support it in such a way in the slides that you are free to skip it without it harming the presentation. You can then decide, on the spot and based on your read of the room and intuition, to use it or leave it out. Jokes bomb for lots of reasons, so don't try to lean on it too heavily, regardless, and don't set yourself up for needing the joke to kill to give a good impression.