As error indicates, the DML is skipping but DDL goes ahead and temporary table is created. 


Also, following succeeds (also a workaround).

MySQL [test]> commit;
ERROR 1213 (40001): Deadlock found when trying to get lock; try restarting transaction
MySQL [test]> show create table test_bug;
+----------+------------------------------------------------------------------------------------------------------+
| Table    | Create Table                                                                                         |
+----------+------------------------------------------------------------------------------------------------------+
| test_bug | CREATE TEMPORARY TABLE `test_bug` (
  `id` int(11) DEFAULT NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8 |
+----------+------------------------------------------------------------------------------------------------------+
1 row in set (0.00 sec)

MySQL [test]> start transaction;
Query OK, 0 rows affected (0.01 sec)

MySQL [test]> insert into test_bug select * from test_bug_source;
Query OK, 1 row affected (0.01 sec)
Records: 1  Duplicates: 0  Warnings: 0

MySQL [test]> commit;
Query OK, 0 rows affected (0.00 sec)



========================================

So the problem seems to occur when:

a) there is an explicit TEMPORARY TABLE

b) DML and DDL occur in same statement


Hence, following succeeds as well
========================================
MySQL [(none)]> drop database test;
Query OK, 1 row affected (0.01 sec)

MySQL [(none)]> create database test;
Query OK, 1 row affected (0.00 sec)

MySQL [(none)]> use test;
Database changed
MySQL [test]> DROP TABLE IF EXISTS test_bug_source;
Query OK, 0 rows affected, 1 warning (0.00 sec)

MySQL [test]> CREATE TABLE test_bug_source(`id` int);
Query OK, 0 rows affected (0.01 sec)

MySQL [test]>
MySQL [test]> INSERT INTO
    ->   test_bug_source
    -> VALUES
    ->   (1)
    -> ;
Query OK, 1 row affected (0.00 sec)

MySQL [test]> COMMIT;
Query OK, 0 rows affected (0.00 sec)

MySQL [test]> START TRANSACTION;
Query OK, 0 rows affected (0.00 sec)

MySQL [test]> DROP TEMPORARY TABLE IF EXISTS test_bug;
Query OK, 0 rows affected, 1 warning (0.00 sec)

MySQL [test]>  CREATE TEMPORARY TABLE test_bug like test_bug_source;
Query OK, 0 rows affected (0.01 sec)

MySQL [test]> commit;
Query OK, 0 rows affected (0.00 sec)

MySQL [test]> show create table test_bug;
+----------+------------------------------------------------------------------------------------------------------+
| Table    | Create Table                                                                                         |
+----------+------------------------------------------------------------------------------------------------------+
| test_bug | CREATE TEMPORARY TABLE `test_bug` (
  `id` int(11) DEFAULT NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8 |
+----------+------------------------------------------------------------------------------------------------------+
1 row in set (0.00 sec)

MySQL [test]> start transaction;
Query OK, 0 rows affected (0.00 sec)

MySQL [test]> insert into test_bug select * from test_bug_source;
Query OK, 1 row affected (0.00 sec)
Records: 1  Duplicates: 0  Warnings: 0

MySQL [test]> commit;
Query OK, 0 rows affected (0.00 sec)
==============================================================