'Node Graph Out of Date'
Digging around various forums comes up with a myriad of answers to this issue.
Some of which can be taken with a grain of salt... (Google is your friend)
The Node Graph is used by the AI in game to set the waypoints for bots, and will rebuild them automatically if they dont already exist. Unless you are using bots, it will have no effect on the map being played.
Possible causes per other forums...
64bit Windows ::: Adding -32bit to your TF2 execution string may fix it.
max_players set too low ::: Set your max_players to something greater than 1.
warez ::: Apparently illegal copies of Valve's games throw this error a lot. If this is the problem, the fix is obvious.
Valve Dev. Wiki says...
This is easy to get rid of. Place an NPC and an info_node into your map. Run it once. As long as you don't modify it, it'll never come back. Its simply telling you that the its building the AI's movement and interaction info. with no info_nodes it tells you every time you start up. with info_nodes and an npc it tells you once. Until you replace the files.
Which seems odd, as TF2 does not typically use NPCs. (correction, I guess the tr_ maps do)
Look into these and see if any of them help.
Otherwise, its just an annoyance, and will not affect the map at all.