I know there were planes used by Germans to trap them troops at the beaches. But assuming they've all gathered at one place in massive numbers, if one bomb dropped onto the most vital part, they could've been all killed very easily! Instead he let most of them escape.
I think you're rather overestimating the destructive power of bombs; short of a nuclear weapon "one bomb" won't kill hundreds of thousands, no matter how tightly they cluster up.
The Luftwaffe did attack evacuating ships (see e.g. /u/thefourthmaninaboat on [How vulnerable were the British naval ships at Dunkirk to aerial attacks?] (https://www.reddit.com/r/AskHistorians/comments/6ozlp6/how_vulnerable_were_the_british_naval_ships_at/)) and troops on the beaches, but between the weather, the smoke from burning oil tanks, the RAF and anti-aircraft fire it was hardly trivial. On the beaches, sand absorbs some of the blast from bombs:
"In some ways, the sand was our saving grace, because the average type of bomb, hitting a hard surface like a roadway, the shrapnel scatters, and you all get it. Going into the sand, there was a thud, and you'd get covered in clods of sand but that was about it. It was still bloody unpleasant." (Lance Corporal John Wells in Joshua Levine's Forgotten Voices of Dunkirk).
/u/thefourthmaninaboat posted about this some time ago. Here's an answer from last year that lays it out well.
Two main reasons, first being that bombers were not accurate and not suited for precision bombing on individual formations of soldiers, but instead bombed general areas and had varying effect at that. Bombers were a menace to be sure, especially when their targets were the evacuation ships such as the Destroyer Grenade and many others, as well as the bombing of harbors the ships could dock at, but the low accuracy of these bombs weren't a solid answer to wiping out an opposing force entirely.
Second was that Dunkirk was within flying range of RAF planes stationed across the Channel in Dover, and provided air cover for the evacuation and downing over 150 German fighters and bombers over the course of the evacuation. While the RAF experienced high losses and neither side could claim full superiority over the air, the presence of these fighters alone, and their ability to sortie out from Dover easily, caused to Germans to take a demure approach when it came to bombing Dunkirk, likely trying to save their own planes.
Norman Franks has a worthwhile work solely focusing on the air component of Operation Dynamo, definitely check it out.
Franks, Norman. Air Battle for Dunkirk. Grub Street. (2006)
edit: added name to the poster of the reference link