Generally speaking the bike has always made those noises except with the stock pipes which are designed to actually muffle the sound you don't really hear it. Aftermarket pipes are usually designed to make the bike louder so naturally you will hear noises like this more.
However, if you installed a full system you have most like thrown off the air/fuel ratio which will require either an ECU reflash or the cheaper more common alternative, a Power Commander to reduce these "popping" noises (also known as after fire)
If you just installed "slip-ons" (no header change and/or catalytic converter removal) you should be fine with out a Power Commander and these noises are not an issue. Some will say throw a Power Commander anyway and it may reduce the popping slightly.