Honda break in oil has a high moly content which is supposed to stay in until the Maintenance Minder indicates needing a change - in theory your oil analysis should show that. I would suggest that the silicone shows your engine is still breaking in. You're not the first to do an early change and certainly the impact of the break in oil decreases as mileage increases. But just be aware that technically you didn't allow your engine to fully break in, according to Honda, and the impact of that is unknown.I changed my CRV's oil and filter at 5,000 miles, and decided to have the oil analyzed by POLARIS Laboratories (eoilreports.com). The 5,000 miles was mostly interstate, and all in warm to hot weather. According to the report, Fuel Dilution is 5% (by volume). There's also a lot of Silicon in the sample (162 ppm), which I hope is seals or casting debris that will fade over time.
I'll redo the oil/filter change and analysis at 10,000 miles.
I love the car, but will carefully document the oil contamination.
Less likely, it could be due to outside contamination and you might take a peek at your engine air filter just to make sure it is seated well, not torn and isn't allowing dust through.