Some Arab countries as well as Iran prohibit travel to Israel in order to issue a visa. I don't think Israel prohibits any stamps but definitely one might get extra attention depending on what countries stamps are in the passport.

For me, crossing the Jordan/Israel border was not a hassle but the security team at Eilat Airport definitely did NOT like me having Indonesian stamps in the passport. I spent 1.5 being interrogated by then and never in my life received such rude treatment (and I've been robbed before when abroad)! They took all my possessions and I was forced to fly without my passport or even my wallet... it was all checked in for my Eilat to TLV flight. My camera got broken with the way they threw it down and threw bins on top of it and they kept my camera battery. I was actually yelled at more abrasively than anybody ever yelled at me WHY DON'T YOU SPEAK ARABIC? THE DEAD SEA IS ONLY IN ISRAEL - NOT IN JORDAN - HOW COULD YOU HAVE BEEN THERE? Etc. etc. And mind you I'm a 30-something white American guy so I don't know what they thought I was going to do or what sort of weapons and bombs I had acquired in the 5 minute taxi ride from the border (where I was checked) and the airport.

When leaving TLV, I got questioned again for about an hour. The focal reason seemed to be Indonesian, Malaysian, and Jordanian stamps but they were very professional and courteous so I didn't mind at all. They were just doing their job.