TN Renewal & Green card process

Hi all,
I just got back the San Diego P.O.E and got my TN Visa renewed.
The Officer informed me that I "may be rejected in the future !" I have worked on a TN for 4 years .went back to Canada for 2 years .and now working with the same employer on my third visa.
Both my wife and myself work with the same employer as a registered nurses and are trying to get them to sponsor us.
They don't seem to be to willing to help us get a green card at this point!

Is it a big deal for my employer to help me with this green card process?

Can the Officers "mark" my file to make if difficult in the future to renew?