I get probably five times as many punctures in my rear wheel as opposed to my front wheel. I run a good pressure and don't get obvious pinch flats.
Does anyone have a logical reason why this could be happening?
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The back wheel is the wheel bearing most of the weight and also the wheel providing the driving force. For these 2 reasons it is likely that the forces being exerted between the wheel and surface are much greater on the rear wheel than on the front. This makes it more likely that you will get punctures on the rear wheel than the front - all other things equal.
It is possible that something is stuck in your rear wheel tire. That piece of glass or metal can pierce the tube repeatedly, even after you repair the tube. This happened to me once. I repaired the hole in the tube and a day later another pressure loss. I finally realized that a piece of glass was stuck in the tire. You can feel with your fingers on the inside of the tire for sharp objects.
Other effects: the front tyre can disturb something lying flat on the ground, flicking it up ready to cause a puncture on the rear; and taking a rear wheel off to fix a flat is more hassle because of the gears and so even if you have equal numbers of flats, the extra time spent on rear ones makes it feel like you have more rear ones :-)
In the past year, have gotten 5 rear flats and 0 front, while riding in bike lanes. 3 flats were caused by small metal pieces, 1 by a thorn, and 1 by a screw. Suspect that the front wheel lifted up these items and the rear wheel rode over them at a puncture angle (straight into the tire). This must be happening since the metal items would normally lay flat on the ground, explaining why flats are on the rear. Am riding 20+ mph, which means the rear tire passes over where the front was very quickly.
Are the holes on the inner surface of the inner tube as opposed to the outer surface. It could be that one of your spokes is slightly loose, when you sit on the bike this spoke may be pushing into the tube slightly and causing the punctures.
Check the position of the holes and see if they're inside or outside, if they're outside then check for sharp objects pushing through the tyre as previously mentioned by someone else.
I cut up a leather belt and use it to line the inside of my tyres. Its a trick my grandad showed me 20 year ago... Its not puncher proof but they are rare.
hope this helps you.
Also wrap tape around the wheel to put a barrier between your spokes and inner tube because they can pinch your tubes causing them to deflate.