Fix Step Flashing
Step flashing is used along walls that intersect the roof. Each short section of flashing channels water over the shingle downhill from it. But if the flashing rusts through, or a piece comes loose, water will run right behind it, and into the house it goes. Rusted flashing needs to be replaced. That means removing shingles, prying siding loose, and then removing and replacing the step flashing. It's that simple. But occasionally a roofer forgets to nail one in place and it eventually slips down to expose the wall. Check out this article for more on installing your own step flashing.
Don't Count on Caulk!
Rarely will caulk or roof cement cure a roof leak?at least for very long. You should always attempt a 'mechanical' fix whenever possible. That means replacing or repairing existing flashing instead of using any type of sealant. Only use caulk for very small holes and when flashing isn't an option.
Fix Small Holes
Tiny holes in shingles are sneaky because they can cause rot and other damage for years before you notice the obvious signs of a leak. You might find holes left over from satellite dish or antenna mounting brackets or just about anything. And exposed, misplaced roofing nails should be pulled and the holes patched. Small holes are simple to fix, but the fix isn't to inject caulk in the hole. You'll fix this one with flashing.