The warning is just a warning telling you that a function(the map) inside a loop referring to outside vars "may" cause an issue. In this case it will not, so can be ignored.
As to your result, seems strange as when i drop the function in your flow I get a result
[{"id":"e061ca3d.2e315","type":"inject","z":"bf9e1e33.030598","name":"Go","props":[{"p":"payload"},{"p":"topic","vt":"str"}],"repeat":"","crontab":"","once":false,"onceDelay":"","topic":"","payload":"1","payloadType":"str","x":190,"y":2100,"wires":[["203e0898.9e7e2"]]},{"id":"203e0898.9e7e2","type":"function","z":"bf9e1e33.030598","name":"fill numeric array (3 x 4)","func":"//var arr =[25,19,24,18,32,31,24,12,29,22,12,14]\nvar arr = [[1,2,3],[4,5,6],[7,8,9],[10,11,12]];\nmsg.payload = arr;\nreturn msg;","outputs":1,"noerr":0,"initialize":"","finalize":"","x":240,"y":2180,"wires":[["b6b6fec1.94c588","b8a4ae21.613328"]]},{"id":"b6b6fec1.94c588","type":"debug","z":"bf9e1e33.030598","name":"Array raw","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"payload","targetType":"msg","statusVal":"","statusType":"auto","x":490,"y":2140,"wires":[]},{"id":"b8a4ae21.613328","type":"function","z":"bf9e1e33.030598","name":"","func":"let output = []\nlet depth = msg.payload[0].length\n// take the third column\nfor(let i = 0; i < depth; i++){\n let col = msg.payload.map((value) => value[i]);\n output.push(col);\n}\nmsg.payload= output;\nreturn msg;\n","outputs":1,"noerr":0,"initialize":"","finalize":"","x":490,"y":2180,"wires":[["f46fae95.e94f9"]]},{"id":"f46fae95.e94f9","type":"debug","z":"bf9e1e33.030598","name":"desired column","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"payload","targetType":"msg","statusVal":"","statusType":"auto","x":730,"y":2180,"wires":[]}]
output
[[1,4,7,10],[2,5,8,11],[3,6,9,12]]
So it must be something you have added or removed, hard to tell any thing from the image you supplied.