I've had my Madone 4.5 for almost a month now, and I've just recently in the past week had two flat tires. The bike has R3 hard cases and before every ride I pump up the tires (100f / 120b). Both flats were in the rear, and in both cases there was no visible debris that might have caused a puncture. They also came after going over a medium bump. By medium I mean not big enough to feel, but not big enough to give me concern to slow down or be lifted from my seat.
I've been pretty hard since I got the bike, riding 15 miles a day most days. My first flat I shook off as a one off. But the second a days later has me thinking, am I riding on the wrong tires?
These events have taught me the valuable lesson of being prepared, and how to change a flat. The first flat was 1-1/2 miles from my car, and being a newbie I had no patches or replacement tube. I had to walk back to my car in my socks for fear of ruining my bike shoes. Ended up with blisters on the bottom of both feet.
When I took it to the bike shop I had them fix it and picked up two replacement tubes. When the second flat came I thought I was prepared. I dreaded taking off the rear wheel, but that wasn't a problem. I managed to puncture one of the replacement tubes during my frantic attempt to solve the proble with too much muscle. Then I watch a quick vid on how to and managed to install the second one. Slightly inflating the tube before inserting it was key .