diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7fe2cbe..075b997 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,8 @@ Bug fixes:
   Preserve line terminators when using `-r/--replace` flag.
 * [BUG #3108](https://github.com/BurntSushi/ripgrep/issues/3108):
   Fix a bug where `-q --files-without-match` inverted the exit code.
+* [BUG #3131](https://github.com/BurntSushi/ripgrep/issues/3131):
+  Document inconsistency between `-c/--count` and `--files-with-matches`.
 * [BUG #3140](https://github.com/BurntSushi/ripgrep/issues/3140):
   Ensure hyphens in flag names are escaped in the roff text for the man page.
 * [BUG #3155](https://github.com/BurntSushi/ripgrep/issues/3155):
diff --git a/crates/core/flags/defs.rs b/crates/core/flags/defs.rs
index c5a7fad..e9b05df 100644
--- a/crates/core/flags/defs.rs
+++ b/crates/core/flags/defs.rs
@@ -1276,6 +1276,14 @@ is a match. The \flag{with-filename} flag can be used to force printing the
 file path in this case. If you need a count to be printed regardless of whether
 there is a match, then use \flag{include-zero}.
 .sp
+Note that it is possible for this flag to have results inconsistent with
+the output of \flag{files-with-matches}. Notably, by default, ripgrep tries
+to avoid searching files with binary data. With this flag, ripgrep needs to
+search the entire content of files, which may include binary data. But with
+\flag{files-with-matches}, ripgrep can stop as soon as a match is observed,
+which may come well before any binary data. To avoid this inconsistency without
+disabling binary detection, use the \flag{binary} flag.
+.sp
 This overrides the \flag{count-matches} flag. Note that when \flag{count}
 is combined with \flag{only-matching}, then ripgrep behaves as if
 \flag{count-matches} was given.
@@ -2184,6 +2192,14 @@ impl Flag for FilesWithMatches {
         r"
 Print only the paths with at least one match and suppress match contents.
 .sp
+Note that it is possible for this flag to have results inconsistent with the
+output of \flag{count}. Notably, by default, ripgrep tries to avoid searching
+files with binary data. With this flag, ripgrep might stop searching before
+the binary data is observed. But with \flag{count}, ripgrep has to search the
+entire contents to determine the match count, which means it might see binary
+data that causes it to skip searching that file. To avoid this inconsistency
+without disabling binary detection, use the \flag{binary} flag.
+.sp
 This overrides \flag{files-without-match}.
 "
     }
diff --git a/tests/binary.rs b/tests/binary.rs
index fd145ce..73639c1 100644
--- a/tests/binary.rs
+++ b/tests/binary.rs
@@ -429,3 +429,40 @@ hay:1867:\"And yet you say he is not a medical student?\"
 ";
     eqnice!(expected, cmd.stdout());
 });
+
+// See: https://github.com/BurntSushi/ripgrep/issues/3131
+rgtest!(
+    matching_files_inconsistent_with_count,
+    |dir: Dir, _cmd: TestCommand| {
+        let mut file1 = String::new();
+        file1.push_str("cat here\n");
+        for _ in 0..150_000 {
+            file1.push_str("padding line\n");
+        }
+        file1.push_str("\x00");
+
+        dir.create("file1.txt", &file1);
+        dir.create("file2.txt", "cat here");
+
+        let got = dir.command().args(&["--sort=path", "-l", "cat"]).stdout();
+        eqnice!("file1.txt\nfile2.txt\n", got);
+
+        // This is the inconsistent result that can't really be avoided without
+        // either making `-l/--files-with-matches` much slower or changing
+        // what "binary filtering" means.
+        let got = dir.command().args(&["--sort=path", "-c", "cat"]).stdout();
+        eqnice!("file2.txt:1\n", got);
+
+        let got = dir
+            .command()
+            .args(&["--sort=path", "-c", "cat", "--binary"])
+            .stdout();
+        eqnice!("file1.txt:1\nfile2.txt:1\n", got);
+
+        let got = dir
+            .command()
+            .args(&["--sort=path", "-c", "cat", "--text"])
+            .stdout();
+        eqnice!("file1.txt:1\nfile2.txt:1\n", got);
+    }
+);
diff --git a/tests/regression.rs b/tests/regression.rs
index b3d7fb1..8dd1ba7 100644
--- a/tests/regression.rs
+++ b/tests/regression.rs
@@ -1545,6 +1545,7 @@ rgtest!(
     }
 );
 
+// See: https://github.com/BurntSushi/ripgrep/issues/3139
 rgtest!(
     r3139_multiline_lookahead_files_with_matches,
     |dir: Dir, _cmd: TestCommand| {