When most people "clear their minds," all they're doing is stopping the distractions they're usually addicted to. When the TV is no longer blaring, when the children are tucked away, when we're not having a good laugh, the things that bother us, the things we've been avoiding, tend to float up into the mind. We may not even understand them or be able to point to where they came from.
This is why people who go on long, solitary prayer retreats sometimes run back to civilization screaming.
Unresolved nonsense will bubble up when you're no longer stuffing it down. To have a completely clear mind, you've got to have all your "issues" handled before you sit down, but this isn't really feasible for most people.
Better - you have to be ready for and willing to endure it. Understand that these things will rise and offer them, one by one, to the one in whose presence you're trying to rest. Carefully and with attention, you have unwrapped a wound and the exposure stings. Offer it up to the healer.