diff --git a/src/flows/multi.ts b/src/flows/multi.ts
index 660497a6..a761f82b 100644
--- a/src/flows/multi.ts
+++ b/src/flows/multi.ts
@@ -320,6 +320,8 @@ function maskFleet(
     const knownVisibility = new Map<SlugKey, RepoVisibility>();
     // Private slugs discovery filtered out are masked but never placeholdered.
     const filteredPrivateSlugs: Private<string>[] = [];
+    // parseConfig refuses a bad repos list and misplaced filters before any file is read; a library caller that
+    // builds the config by hand meets the same refusals here.
     if (cfg.reposInput) {
       const parsed = yield* parseReposInput(cfg.reposInput);
       if (parsed.discover) {
diff --git a/src/flows/run-config.ts b/src/flows/run-config.ts
index 1d748817..746da9b9 100644
--- a/src/flows/run-config.ts
+++ b/src/flows/run-config.ts
@@ -5,7 +5,7 @@
  */
 
 import { err, ok, type Result, safeTry } from "neverthrow";
-import { LIST_SEPARATOR } from "../discovery/repos-input.js";
+import { LIST_SEPARATOR, parseReposInput } from "../discovery/repos-input.js";
 import { LAYERINGS } from "../engine/layers.js";
 import type { Problem } from "../problem.js";
 import { PRIVATE_REPORT_CHANNELS } from "../report/delivery.js";
@@ -96,6 +96,28 @@ function readSnapshotBase(input: Inputs, env: ConfigEnv) {
   });
 }
 
+/**
+ * The target problems the inputs alone decide: a repos list that mixes "*" with names or carries a bad entry, and
+ * discovery filters set where no "*" discovery runs. Refused here, before any file is read, so an unreadable
+ * repos-dir cannot hide them; resolveTargets meets the same problems for a library caller that builds the config
+ * by hand.
+ */
+function refuseTargetInputs(
+  reposInput: string,
+  discoveryFiltersSet: readonly string[],
+): Result<void, Problem> {
+  const filtersWithout = (targets: "explicit-repos" | "repos-dir"): Result<void, Problem> =>
+    discoveryFiltersSet.length > 0
+      ? err({ code: "discovery-filters-without-wildcard", filters: discoveryFiltersSet, targets })
+      : ok(undefined);
+  if (!reposInput) {
+    return filtersWithout("repos-dir");
+  }
+  return parseReposInput(reposInput).andThen((parsed) =>
+    parsed.discover ? ok(undefined) : filtersWithout("explicit-repos"),
+  );
+}
+
 /** The file arm: one repository, the fleet inputs refused. */
 function parseSnapshotFileArm(
   input: Inputs,
@@ -175,6 +197,7 @@ function parseSnapshotConfig(
     if (!reposInput && !reposDir) {
       return err({ code: "input-snapshot-dir-without-targets" });
     }
+    yield* refuseTargetInputs(reposInput, filters.discoveryFiltersSet);
     return ok({
       ...base,
       form: "dir" as const,
@@ -276,6 +299,7 @@ export function parseConfig(
       if (settingsFile !== DEFAULT_SETTINGS_FILE) {
         return err({ code: "input-settings-file-with-multi" });
       }
+      yield* refuseTargetInputs(reposInput, discoveryFiltersSet);
       const adminOwner = githubRepository.split("/")[0] ?? "";
       return ok({
         ...common,
diff --git a/test/flows/inputs.test.ts b/test/flows/inputs.test.ts
index 24ba25b4..a85d1941 100644
--- a/test/flows/inputs.test.ts
+++ b/test/flows/inputs.test.ts
@@ -553,3 +553,41 @@ describe("mode: snapshot", () => {
     );
   });
 });
+
+describe("target inputs the file system cannot change", () => {
+  // Before, these were refused inside resolveTargets after the repos directory was read, so an unreadable directory
+  // reported itself and hid the input error; parseConfig never touches the directory.
+  const FLEET = { GITHUB_REPOSITORY: "admin/fleet" };
+  test.each<[string, Partial<Record<InputName, string>>, Problem]>([
+    [
+      "a repos list mixing * with names",
+      { repos: "*,o/r" },
+      { code: "repos-input-wildcard-mixed" },
+    ],
+    [
+      "a repos list with a bad entry",
+      { repos: "o/r,not-a-slug" },
+      { code: "repos-input-invalid-entries", invalid: ["not-a-slug"], duplicated: [] },
+    ],
+    [
+      "discovery filters beside explicit repos",
+      { repos: "o/r", forks: "exclude" },
+      { code: "discovery-filters-without-wildcard", filters: ["forks"], targets: "explicit-repos" },
+    ],
+    [
+      "discovery filters beside repos-dir alone",
+      { "repos-dir": "repos", forks: "exclude" },
+      { code: "discovery-filters-without-wildcard", filters: ["forks"], targets: "repos-dir" },
+    ],
+  ])(
+    "%s is refused when the inputs are parsed, for apply and for a snapshot dir",
+    (_case, inputs, problem) => {
+      expect(rejection(parse({ token: "t", ...inputs }, FLEET))).toEqual(problem);
+      expect(
+        rejection(
+          parse({ token: "t", mode: "snapshot", "snapshot-dir": "snaps", ...inputs }, FLEET),
+        ),
+      ).toEqual(problem);
+    },
+  );
+});