It sounds like poor heat transfer from the tip to the part. I keep my desoldering tip tinned or else it goes black and then does poorly heating up things. Your technique might be too fast- put the tip on the pad, squarely on it not crooked, wait a couple seconds for heat to flow to the top side, then hit the vacuum. If that doesn't pull all the solder, ADD fresh solder to the pad, and re-do but wait longer for the heat to flow to the other side of the board. Careful not to overheat the pad, sometimes leave it to cool down.
Also, lead-free rework can clog things so use the poker when it's hot and push out any slag at the back. You might have low suction.
Best is to practice or troubleshoot a desoldering problem on junk boards.