I found out why 2. happens, and so...

HOW TO MAKE INCREDABLE LARGE REBEL ARMIES!!!

my example is as follows: the kalifah is trapped in Leon with his son, Cordoba and Portugal are mine, I`m neutral and Castile is rebel. If the kalifah and his son would die, it would start a civil war. So I send enough spies into Leon to cause rebellion. The rebel army appears, the kalifah flees to the keep but attacks the rebels after one year siege. His 165 men against 959 rebels, most of them Murabitin, and the rebels withdraw to Castile!!
This happens every time. So I can start another rebellion in Leon and they withdraw to Castile again. Meanwhile there are 3000 rebels in Castile!

Still no idea why 3. happens but it wasn`t civil war. Maybe the AI does bribe rebels sometimes.

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In the name of electricity: CHARGE!!!