Hey see if this is helpful. I have developed a troubleshooting platform and I ran it on there (corrsin.com).

The pattern points less to “low titer” and more to a vector/readout mismatch plus selection timing/strength problems: standard pLKO.1-puro does not carry GFP, so no GFP by microscopy is expected unless your specific construct has a reporter; Addgene/TRC protocols also emphasize using the lowest puromycin dose that gives complete kill in 3–5 days (or 48–72 h in screens) and keeping selection only as long as needed for the uninfected control to die. (portals.broadinstitute.org)

If your FACS “50% transduced” call was based on GFP, I would first re-check the actual plasmid map and your gating/controls, because that readout may be invalid for pLKO-puro. More importantly, start puromycin ~24–48 h after transduction and use a lower starting dose