Something to keep in mind here is that Kushner works in the White House. Donald Trump Jr. does not. There are different levels of sensitivity here when it comes to how these things play out today in 2017 (regardless of what may have happened at a point in 2016 when Donald Trump wasn’t even the Republican nominee yet).
Swirling behind the scenes is the idea that kushner was likely to work in WH and Jr was not. Kushner has to fill out forms. Jr does not.
This could have effected all kinds of things...like..oh we can just blame Jr if something comes out strategy.
There is that rumor that Kushner is on tape saying it. The rumor could be psy ops to get Jr to flip. .become paranoid..etc. his new lawyer is a mafia lawyer who will be well familiar with tactics
...and also, Don Jr took that meeting as a private citizen with no prior experience in government or any working knowledge of the protocols involved in contact with foreign agents (lobbyists).
Manafort should have had a handle on this meeting. Seems to me, he was asleep on the job.