It happened too quickly.
The North Koreans invaded at dawn on June 25th 1950, which is the middle of the afternoon June 24th at UN HQ in NYC. Within 5 hours news agencies had picked it up. 24 hours after the invasion, resolution 82 was introduced and passed. Security Council Resolution 82 demanded hostilities end, and the North Koreans withdraw.
Two days later, Security Council Resolution 83 was passed authorizing UN member militaries to assist South Korea.
The USSR generally abstained anyway.
Their boycott didn't change the situation much. Prior to their UN boycott on January 13th, 1950, the Soviets abstained on most on Security Council resolutions. Of the 78 resolutions prior to the boycott, they abstained or were absent for 43 of them. This is quite unlike the other security council members at the time (except for Ukraine, a Soviet puppet at the time, which also abstained a lot). This suggests they didn't take the UN seriously, didn't see unprecedented military intervention as a possibility, and would be caught on the wrong foot when it happened.
International decision making was slow.
In this day and age of instant world-wide communication and fast jet travel, it's difficult to understand just how slow communications and travel were in 1950. No internet (of course), but even making a long distance phone call was a nightmare. Making one from the US to the Soviet Union was even more difficult.
Jet airliners were still a few years off, if you need to get your UN representative back to New York that means multiple flights on a slow, propeller driven aircraft.
Now imagine the situation for the Soviets. They were well aware the North Koreans were going to invade, they assisted in the planning. And they were concerned the US might intervene. But they probably weren't expecting the untested UN Security Council to take military action. On top of that, Yakov Malik, their ambassador to the UN, had spectacularly walked out of the UN in protest of their seating the representative of Nationalist China over Communist China, and declared a Soviet boycott.
The first the Soviets would learn about a UN intervention would probably be as Security Council Resolution 82 is being passed. The clock is now ticking.
This information has to be encrypted, typed up, sent from NYC to Moscow across multiple communication lines, received, typed up, copied, and sent up the chain of command. Then Moscow has to debate what to do about it.
Is this resolution even a concern? So what if the UN says the war is illegal, what are they going to do about it? The UN is young and untested. It's predecessor, the League Of Nations, was spectacularly ineffective in stopping aggression prior to WWII. The Soviets had a habit of successfully running roughshod over international treaties.
Then, if they do decide it's a concern, they have to debate whether that possibility is worth ending their UN boycott and possibly angering Communist China.
If they decide to return their ambassador to the UN, it has to be typed up, sent down the chain of command, encrypted, transmitted back to NY over multiple communications channels, received, decrypted, typed up, given to the relevant people, who then have to decide what to do about it.
Once that's all done, Yakov Malik has to get to UN HQ from wherever he was at the time. Considering the boycott began in January, he might not even have been in NYC or even the US at the time.
All in two days.
This answer is quite speculative, knowing the actual deliberations within Soviet High Command and the location of Yakov Malik at the time would lend it some more weight. But it's quite useful to understanding the scenario the Soviets faced and how difficult and slow international politics was in 1950. It's not like today where people would hear the news within minutes, decisions would be made within hours, with frantic phone calls back and forth, and ambassadors hopping onto jets to be in NYC in 8 hours.
The US, with the UN HQ right in their backyard and driving the whole process, had a serious home field advantage.