I managed to run the tests in one of the bots. Here are the diffs of the tests:

--- /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/cursor-request-cycle-expected.txt
+++ /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/cursor-request-cycle-actual.txt
@@ -55,9 +55,10 @@
 PASS cursor.value is "value2"
 cursor = null
 gc()
-PASS cursorRequestObservation.wasCollected is true
-PASS cursorObservation.wasCollected is true
+FAIL cursorRequestObservation.wasCollected should be true. Was false.
+FAIL cursorObservation.wasCollected should be true. Was false.
 PASS successfullyParsed is true
+Some tests failed.

 TEST COMPLETE

--- /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/cursor-request-cycle-private-expected.txt
+++ /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/cursor-request-cycle-private-actual.txt
@@ -55,9 +55,10 @@
 PASS cursor.value is "value2"
 cursor = null
 gc()
-PASS cursorRequestObservation.wasCollected is true
-PASS cursorObservation.wasCollected is true
+FAIL cursorRequestObservation.wasCollected should be true. Was false.
+FAIL cursorObservation.wasCollected should be true. Was false.
 PASS successfullyParsed is true
+Some tests failed.

 TEST COMPLETE

--- /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/request-size-estimate-expected.txt
+++ /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/request-size-estimate-actual.txt
@@ -15,10 +15,9 @@
 db = event.target.result
 store = db.transaction('store', 'readwrite').objectStore('store')
 request = store.add(createObject(), randomKey(keySize))
-PASS 'error' in request is true
-PASS request.error.code is DOMException.QUOTA_EXCEEDED_ERR
-PASS request.error.name is "QuotaExceededError"
+FAIL Add operation should fail because task size is bigger than space available
 PASS successfullyParsed is true
+Some tests failed.
 TEST COMPLETE

--- /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/result-request-cycle-expected.txt
+++ /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/result-request-cycle-actual.txt
@@ -32,9 +32,10 @@
 PASS resultObservation.wasCollected is false
 result = null
 gc()
-PASS getRequestObervation.wasCollected is true
-PASS resultObservation.wasCollected is true
+FAIL getRequestObervation.wasCollected should be true. Was false.
+FAIL resultObservation.wasCollected should be true. Was false.
 PASS successfullyParsed is true
+Some tests failed.

 TEST COMPLETE

--- /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/storage-limit-expected.txt
+++ /home/slave/webkitgtk/gtk-linux-64-release/build/layout-test-results/retries/storage/indexeddb/storage-limit-actual.txt
@@ -27,11 +27,9 @@
 store.add(new Uint8Array(1), 9).onsuccess = ()=> { ++addCount; }
 store.add(new Uint8Array(1), 10).onsuccess = ()=> { ++addCount; }
 request = store.add(new Uint8Array(409601), 0)
-PASS addCount is 10
-PASS 'error' in request is true
-PASS request.error.code is DOMException.QUOTA_EXCEEDED_ERR
-PASS request.error.name is "QuotaExceededError"
+FAIL Add operation should fail because storage limit is reached, but succeeded.
 PASS successfullyParsed is true
+Some tests failed.

 TEST COMPLETE

It also happens to me that I got some of these tests passing locally (in my case I got 2 failures and 3 passes).

Fixed by r260322. Updated expectations in r260389.