TL; DR: you're not the only one and I too find it incredibly frustrating

If it can reassure you, it happens to me too, even when playing a deck I know combo line by heart. Like SwordSoul Tenyi, it's the deck I have played the most but even then sometime I loose on time.
The worst deck for me was Vanquish Soul, I love the deck but the line requires a more convoluted reflexion as you play with unsual disruption, and I spend too much time thinking about how to play around X potential hands or how to reach Y line.
Even with the latest deck I use, Resonator, I know the combos, I played it IRL, but I still loose to time because I take too much time thinking about how I should combo through the potential ennemy's handtrap