This problem appered when I was checking out older tag from the Chromium project.
Working with Release Branches

~/chromium_build/src$ git fetch --tags
~/chromium_build/src$ git checkout -b tag_35.0.1849.0 35.0.1849.0
~/chromium_build/src$ gclient sync --with_branch_heads --jobs 16

Error log:

Syncing projects: 100% ( 1/ 1) src

src (ERROR)
----------------------------------------
[0:00:00] Started.

________ running 'git reset --hard HEAD' in '/home/sam.chen/chromium_source/src'
[0:00:00] HEAD is now at 77bd011 Publish DEPS for Chromium 35.0.1849.0
[0:00:00] _____ src : Attempting rebase onto 77bd011602b1799f715591e697806c55e7ef8b7f...
[0:00:00] Current branch tag_35.0.1849.0 is up to date.
[0:00:00]
----------------------------------------
Error: 1> Dependency src specified more than once:
1>   src(https://chromium.googlesource.com/chromium/src.git) [https://chromium.googlesource.com/chromium/src.git]
1> vs
1>   src(https://chromium.googlesource.com/chromium/src.git) -> src(https://chromium.googlesource.com/chromium/src.git@ae69ae7642
35ccaac55fc44a3b5f3276ff34cb58) [https://chromium.googlesource.com/chromium/src.git@ae69ae764235ccaac55fc44a3b5f3276ff34cb58]

You need to edit the .DEPS.git file, remove the entry ‘src’ and then gcient sync --with_branch_heads.

~/chromium_build/src$ git diff .DEPS.git
diff --git a/.DEPS.git b/.DEPS.git
index aa9f7a2a..81e870b 100644
--- a/.DEPS.git
+++ b/.DEPS.git
@@ -31,8 +31,6 @@ deps = {
         Var('git_url') + '/chromium/tools/commit-queue.git@7779c66e03aa5b87a2d7354387b3d16338da9e29',
     'depot_tools':
         Var('git_url') + '/chromium/tools/depot_tools.git@9a8b066e52dff833016db0fcea69072814162ffe',
-    'src':
-        Var('git_url') + '/chromium/src.git@ae69ae764235ccaac55fc44a3b5f3276ff34cb58',
     'src/breakpad/src':
         Var('git_url') + '/external/google-breakpad/src.git@d7b5ea03d763b25445c198963034b49596da45f0',
     'src/chrome/browser/resources/pdf/html_office':

~/chromium_build/src$ gclient sync --with_branch_heads --jobs 16 --force

Reference:
https://groups.google.com/a/chromium.org/forum/#!msg/chromium-dev/1iNTFLNjUQo/LgCPaxkbd-4J