This is absolutely normal for about any internal combustion engine. There's a lot of soot and other particles suspended in the oil. Every drop of old oil that remains during an oil change will immediately stain the new stuff black. One of the main jobs of engine oil is keeping the cylinder walls clean, so it will never stay golden for long.

Tl;dr: engine oil is supposed to do this, don't worry.

This is not unusual. A few things to consider:

One, motorcycles and their wet clutches fill their oil with particulate gumpf very quickly compared to other engines. This will make your oil dark very quickly.

"But I didn't use my clutch at all just then," you say. True, but you also can't get all of the old oil out of your crankcase without truly heroic efforts, and what's left in there will be quite black. There's also not much oil volume in a motorcycle crankcase, only a quart or two in most cases, so the proportion of old stuff vs. new stuff is actually pretty high and this'll be visibly apparent right away.