Charging a furnace minecart with a fuel item while it's toggled off (sitting on an unpowered rail) adds the fuel to the pauseFuel value instead, but that value is not clamped to a maximum, so when the minecart is toggled on again, the fuel displayed is negative.

Testing it, it might just be a visual bug, because as the fuel decreases, it rolls back into the positives and works properly. Regardless, from a game balance perspective it might be a good idea to have a ceiling on how much fuel you can add to a furnace minecart.

Also, when toggling the furnace minecart back on, often the furnace does not start moving again as expected. It only works on the X axis, not on the Z axis. Looking at the code, this might be the culprit:

else if (fabrication$pauseFuel > 0) {
	fuel += fabrication$pauseFuel;
	fabrication$pauseFuel = 0;
	Direction dir = this.getMovementDirection();
	pushX = dir.getOffsetX();
	pushZ = dir.getOffsetY(); // instead of getOffsetZ
}

One final note, it would be cool to have a way to automate refueling a furnace minecart when it's toggled off, because otherwise it would be impossible to make a proper automated system using them. I expected hoppers or dispensers to work, but they don't.