The problem is that the entire amount of this distribution was required to have been deposited into the traditional IRA; the IRA custodian erred in allowing you to divert part of it elsewhere. (Note that if the entire amount was deposited into a non-IRA account before some portion of the distribution was deposited into the traditional IRA, none of the distribution was directly rolled over.)
Under the circumstances, the Form 1099-R is incorrect. However, because the 401(k) apparently did what you told them to do, they likely will be unwilling to issue a corrected Form 1099-R to reflect what actually happened, but you must try before preparing substitute Forms 1099-R (Forms 4852) to reflect what actually happened.
Two Forms 1099-R will be needed to show what actually happened. The code G Form 1099-R will need to be changed to reflect the amount actually directly rolled over and a separate code 1, 2 or 7 Form 1099-R (depending on your age and your age when you left service with this employer) will be needed for the portion not rolled over. (If you were under age 55 in 2020, code 1 will be the code,) This code 1, 2 or 7 Form 1099-R will have the same amount in box 2a as is in box 1.
Alternatively, as long as the money was deposited into the traditional by the 60th day following the date of the distribution from the 401(k) or, if distributed after January 31, no later than July 15, you can use a single substitute code 1, 2 or 7 Form 1099-R with the entire gross amount of the original shown in both boxes 1 and 2a, treating the entire distribution as an indirect rollover. You'll then be able to report the distribution as described by DanaB27.
