chore: add note of autoplan modules limitation (#3166)

runatlantis.io/docs/server-configuration.md

@@ -170,6 +170,10 @@ Values are chosen in this order:
 By default, changes to modules will not trigger autoplanning. See the flags below. 
 :::
 
+::: warning NOTE
+If any projects are defined in a repo atlantis.yaml file, the logic for this flag will not execute. See issue [#3122](https://github.com/runatlantis/atlantis/issues/3122).
+:::
+
 ### `--autoplan-modules`
 
 ```bash
@@ -183,6 +187,10 @@ Included project are projects with files included by `--autoplan-file-list`.
 After tracing, Atlantis will plan any project that includes a changed module. This is equivalent to setting
 `--autoplan-modules-from-projects` to the value of `--autoplan-file-list`. See below.
 
+::: warning NOTE
+If any projects are defined in a repo atlantis.yaml file, the logic for this flag will not execute. See issue [#3122](https://github.com/runatlantis/atlantis/issues/3122).
+:::
+
 ### `--autoplan-modules-from-projects`
 
 ```bash