Carbon has to be sealed completely from aluminum or the epoxy can start corroding the metal quite significantly. It's a manufacturing defect, not a use issue, and this was common in frames from around this period. It's caused by the very caustic nature of carbon resin when it isn't insulated from the aluminum.
Carbon/aluminum corrosion is absolutely a real thing, but this is not quite how it works. The resin isn't particularly caustic, although I wouldn't mainline the stuff. The problem is that when you put carbon next to aluminum, you've created a battery. When carbon and aluminum swap electrons, the aluminum corrodes and the bond between the two fails.
As 11.4 notes, this was a problem on early (late '80s-early '90s) carbon frames. If you look at the old Giant Cadex frames, you'll see that the aluminum bottom bracket shells are hard anodized. The anodization is an excellent electrical insulator and prevents galvanic corrosion with the adjacent carbon.
Here's a more detailed explanation from http://www.boeing.com/commercial/aeroma ... rrosn.html
For example, graphite fibers, which are used to reinforce some plastic structure, present a particularly challenging galvanic corrosion combination. The fibers are good electrical conductors and they produce a large galvanic potential with the aluminum alloys used in airplane structure. The only practical, effective method of preventing corrosion is to keep moisture from simultaneously contacting aluminum structure and carbon fibers by finishing, sealing, using durable isolating materials such as fiberglass, and providing drainage.
You can scrape the paint off and see what's under there, sure. Corroded (oxidized) aluminum typically looks white and powdery.
In my opinion, your frame is so recent and made by such an experienced manufacturer of carbon-bonded-to-aluminum frames (Merida) that galvanic corrosion is an unlikely culprit. Furthermore, there's lots of corrosion far from the carbon stays; galvanic corrosion would start at the carbon/aluminum interface and radiate outward.
Many alloys of aluminum corrode like crazy in the presence of salt water. If you rode this bike in the winter and didn't rinse off all the road brine, I'd expect to see corrosion like this. If this is a non-galvanic corrosion issue, it's really not a manufacturing defect, so I wouldn't expect Merida to warranty the frame.
But there's a fair chance that your frame is structurally sound and just needs to have the corrosion removed with, say, a wire brush. Structural integrity is impossible to assess without putting hands on the frame. If I were you, I'd take it to a shop I trusted for an opinion.
Speaking of trusting shops, why on earth are you running the cables without a guide? They will certainly abrade your paint and provide a great place for new corrosion to start.