The best example I'm aware of was in 2002, when redistricting in Michigan following the 2000 Census caused Rep. Lynn N. Rivers to lose her 13th district. The majority of its area was merged into the neighboring district, represented by fellow Democrat John Dingell, a Michigan representative for almost 50 years. Rivers challenged Dingell in the primary for the 15th district and was supported by Pelosi with a donation of $10,000.
This incident is described by Vincent Bzdek in his biography of Pelosi - Woman of the House: The Rise of Nancy Pelosi:
Her emphasis on holding people accountable was a break from the
leadership of the immediate past, congressional observers said. “She
is not afraid to tell people what she wants them to do and hold them
accountable,” said one aide close to the Speaker. This is the “gavel”
part of her leadership style.
She made a point of waving that gavel even before she was elected,
when she contributed $10,000 to Lynn Rivers in a Michigan primary
against the longest-serving House member, John D. Dingell, who had
announced his support of Hoyer. Dingell complained that it was
unprecedented for a member of the House Democratic leadership to favor
one candidate over another in a primary.
Pelosi’s staff defended the donation by saying at the time it was
given, it wasn’t clear that a new redistricting plan would pit Rivers
against Dingell. The donation was handed out in September 2001, one
day before the new district borders were signed into law. And it
didn’t help Rivers much: Dingell won the primary anyway. Some of
Pelosi’s allies, however, said she was clearly sending a message about
loyalty, much the way she would a few years later when she backed her
longtime ally John Murtha for majority leader, even though she
probably knew he was going to lose. For many in the caucus, the
contribution announced in no uncertain terms there would be
retribution for disloyalty.
Apart from this, I'm not aware of any other instances where Pelosi supported a challenger to a Democratic incumbent in a primary for a congressional seat.