Abaddon is defeated by a Imperial Navy Admiral in the Imperial campaign. On top of that a random Necron Overlord killed Gulliman and Abaddon in the Necron campaign. It's quite absurd.
This is navel warfare though, it's kinda ridiculous to suggest that whatever ship that a primarchs is on is automatically invincible just because they are on board.
There were many cases in the Great Crusade where the Primarchs found themselves in sticky situations that were difficult to extract themselves. Apart from their youths like Angron being made a slave, some examples include: being trapped by cave-ins (Roboute on Thoas, Jagatai Khan on Prospero, Ferrus Manus on Caldera), being trapped on ships in enemy boarding actions (Rogal Dorn in his demise), or extremely powerful foes. Magnus the Red, the great psyker primarch, supported by some of his most elite Sekhmet Honour guard (themselves elite class psykers) were overpowered in a buried dark age ship by the Shaitan, a gestalt of a thousand vengeful psykers executed painfully by the locals during Old Night. It overwhelmed his own psychic might, burned and flayed and exploded many of his honour guard, and he barely got away with having himself executed by the wicked dark age machinery and his soul extracted to join the Shaitan.
It's actually rather easy to do if you have like 90 terminators against the primarch alone, they've captured Guilliman soon after he left Ultramar for a few moments before another group bailed them out. Lore wise it won't happen just cause these are superheroes of the setting. But that's cause of the authors and plot armor. Physically in universe you just need enough marines to bind them.
Guilliman: I have a decorative ram in my X kilometers long ship. Abbadon: 5:48 RAM THAT ONE! and the one behind it also! and scratch the hull side of this other one! Bruh, imperial fleet ships with the ram's are OP. Point you 1.2k health ship into a fleet of tyranids and watch them get deleted into the ram meat grinder.
Imagine being late for an important meeting with the Warmaster... you make him wait like 10 minutes... His chill is absolute zero... the outcome would be horrifying...
