maria-5.5 (ver 5.5.35-MariaDB-debug-log) shows same behavior.

(gdb) thread apply all bt

Thread 5 (Thread 0xb6bfeb40 (LWP 18122)):
#0 0xb7fdd424 in __kernel_vsyscall ()
#1 0xb7f649db in read () at ../sysdeps/unix/syscall-template.S:82
#2 0x0890ff15 in vio_read (vio=0xb7442830, buf=0xb77f4030 "\001", size=4)
at maria/bld/5.5/vio/viosocket.c:72
#3 0x08184fc8 in my_real_read (net=0xb421621c, complen=0xb6bfe1e8)
at maria/bld/5.5/sql/net_serv.cc:840
#4 0x08185532 in my_net_read (net=0xb421621c) at maria/bld/5.5/sql/net_serv.cc:1026
#5 0x082222b2 in do_command (thd=0xb4216030) at maria/bld/5.5/sql/sql_parse.cc:739
#6 0x08321fef in do_handle_one_connection (thd_arg=0xb4216030)
at maria/bld/5.5/sql/sql_connect.cc:1266
#7 0x08321aac in handle_one_connection (arg=0xb4216030)
at maria/bld/5.5/sql/sql_connect.cc:1181
#8 0x085655a8 in pfs_spawn_thread (arg=0xb4221fe0)
at maria/bld/5.5/storage/perfschema/pfs.cc:1015
#9 0xb7f5dd4c in start_thread (arg=0xb6bfeb40) at pthread_create.c:308
#10 0xb7d6cbae in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:130

Thread 4 (Thread 0xb7c79b40 (LWP 18118)):
#0 0xb7fdd424 in __kernel_vsyscall ()
#1 0xb7f65be1 in do_sigwait (set=0x8d9bff4, sig=0xb7c792c4)
at ../nptl/sysdeps/unix/sysv/linux/../../../../../sysdeps/unix/sysv/linux/sigwait.c:63
#2 0xb7f65c75 in __sigwait (set=0xb7c79234, sig=0xb7c792c4)
--Type <return> to continue, or q <return> to quit--
at ../nptl/sysdeps/unix/sysv/linux/../../../../../sysdeps/unix/sysv/linux/sigwait.c:100
#3 0x0817a71a in signal_hand (arg=0x0) at maria/bld/5.5/sql/mysqld.cc:3060
#4 0x085655a8 in pfs_spawn_thread (arg=0xb7429b30)
at maria/bld/5.5/storage/perfschema/pfs.cc:1015
#5 0xb7f5dd4c in start_thread (arg=0xb7c79b40) at pthread_create.c:308
#6 0xb7d6cbae in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:130

Thread 3 (Thread 0xb73ffb40 (LWP 18117)):
#0 0xb7fdd424 in __kernel_vsyscall ()
#1 0xb7f61d13 in pthread_cond_timedwait@@GLIBC_2.3.2 ()
at ../nptl/sysdeps/unix/sysv/linux/i386/i686/../i486/pthread_cond_timedwait.S:236
#2 0x088d7516 in safe_cond_timedwait (cond=0x9700120, mp=0x97000a0, abstime=0xb73ff22c,
file=0x8a40898 "maria/bld/5.5/storage/maria/ma_servicethread.c", line=119)
at maria/bld/5.5/mysys/thr_mutex.c:547
#3 0x085ba3f3 in inline_mysql_cond_timedwait (that=0x9700120, mutex=0x97000a0, abstime=0xb73ff22c,
src_file=0x8a40898 "maria/bld/5.5/storage/maria/ma_servicethread.c", src_line=119)
at maria/bld/5.5/include/mysql/psi/mysql_thread.h:1017
#4 0x085ba981 in my_service_thread_sleep (control=0x8db5cb8, sleep_time=30000000000)
at maria/bld/5.5/storage/maria/ma_servicethread.c:118
#5 0x085ae49c in ma_checkpoint_background (arg=0x1e)
at maria/bld/5.5/storage/maria/ma_checkpoint.c:705
#6 0x085655a8 in pfs_spawn_thread (arg=0xb74294f0)
at maria/bld/5.5/storage/perfschema/pfs.cc:1015
#7 0xb7f5dd4c in start_thread (arg=0xb73ffb40) at pthread_create.c:308
--Type <return> to continue, or q <return> to quit--
#8 0xb7d6cbae in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:130

Thread 1 (Thread 0xb7c7b700 (LWP 18113)):
#0 0xb7fdd424 in __kernel_vsyscall ()
#1 0xb7d5e460 in _GI__poll (fds=0xbfffef4c, nfds=2, timeout=-1) at ../sysdeps/unix/sysv/linux/poll.c:87
#2 0x0817ea51 in handle_connections_sockets () at maria/bld/5.5/sql/mysqld.cc:5621
#3 0x0817dcfc in mysqld_main (argc=82, argv=0xb7432c60)
at maria/bld/5.5/sql/mysqld.cc:5070
#4 0x081759fb in main (argc=7, argv=0xbffff1d4) at maria/bld/5.5/sql/main.cc:25

Only debug builds are affected.

This seem to affect mysql-5.7 debug build as well.

$ perl mtr mysqlhotcopy_myisam
Logging: mtr mysqlhotcopy_myisam
MySQL Version 5.7.2
Checking supported features...

• SSL connections supported
• binaries are debug compiled
  Collecting tests...
  Checking leftover processes...
  Removing old var directory...
  Creating var directory '/home/nirbhay/project/repo/mysql/bld/5.7/install/mysql-test/var'...
  Installing system database...
  Using server port 40062

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

TEST RESULT TIME (ms) or COMMENT
--------------------------------------------------------------------------

worker[1] Using MTR_BUILD_THREAD 300, with reserved ports 13000..13009

• • • glibc detected *** mysqlhotcopy: double free or corruption (!prev): 0x09996050 ***
      ======= Backtrace: =========
      /lib/i386-linux-gnu/libc.so.6(+0x75ee2)[0xb7615ee2]
      /usr/lib/perl5/auto/DBD/mysql/mysql.so(mysql_db_destroy+0x45)[0xb7520265]
      /usr/lib/perl5/auto/DBD/mysql/mysql.so(XS_DBD_mysql_db_DESTROY+0x185)[0xb752f6c5]
      /usr/lib/perl5/auto/DBI/DBI.so(XS_DBI_dispatch+0x2e46)[0xb7561706]
      mysqlhotcopy(Perl_pp_entersub+0x487)[0x80e7867]
      mysqlhotcopy(Perl_call_sv+0x670)[0x8075570]
      mysqlhotcopy(Perl_sv_clear+0x515)[0x80edce5]
      mysqlhotcopy(Perl_sv_free2+0x4b)[0x80ee3ab]
      mysqlhotcopy[0x80c810c]
      mysqlhotcopy(Perl_mg_free+0x25)[0x80c8c65]
      mysqlhotcopy(Perl_sv_clear+0x1b4)[0x80ed984]
      mysqlhotcopy(Perl_sv_free2+0x4b)[0x80ee3ab]
      mysqlhotcopy[0x80e8da1]
      mysqlhotcopy(Perl_sv_clean_objs+0x28)[0x80eeb78]
      mysqlhotcopy(perl_destruct+0x1653)[0x80773a3]
      mysqlhotcopy(main+0xfb)[0x805e1cb]
      /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0xb75b94d3]
      mysqlhotcopy[0x805e241]
      ======= Memory map: ========
      ...
      main.mysqlhotcopy_myisam [ fail ]
      Test ended at 2013-12-11 18:31:21

CURRENT_TEST: main.mysqlhotcopy_myisam
Aborted (core dumped)
mysqltest: In included file "./include/mysqlhotcopy.inc":
included from ./include/mysqlhotcopy.inc at line 47:
At line 46: command "$MYSQLHOTCOPY --quiet -S $MASTER_MYSOCK -u root hotcopy_test hotcopy_save" failed

Output from before failure:
exec of '/home/nirbhay/project/repo/mysql/bld/5.7/install/bin/mysqlhotcopy --quiet -S /home/nirbhay/project/repo/mysql/bld/5.7/install/mysql-test/var/tmp/mysqld.1.sock -u root hotcopy_test hotcopy_save' failed, error: 34304, status: 134, errno: 0

The result from queries just before the failure was:
< snip >
INSERT INTO t1 VALUES (1,'aaaaaaaaaaaaaaaaaaaa'),(2, 'bbbbbbbbbbbbbbbbbbbbbbb');
Warnings:
Warning 1265 Data truncated for column 'c2' at row 2
INSERT INTO t2 VALUES (1,'aaaaaaaaaaaaaaaaaaaa'),(2, 'bbbbbbbbbbbbbbbbbbbbbbb');
Warnings:
Warning 1265 Data truncated for column 'c2' at row 2
INSERT INTO t3 VALUES (1,'aaaaaaaaaaaaaaaaaaaa'),(2, 'bbbbbbbbbbbbbbbbbbbbbbb');
Warnings:
Warning 1265 Data truncated for column 'c2' at row 2
db.opt
t1.MYD
t1.MYI
t1.frm
t2.MYD
t2.MYI
t2.frm
t3.MYD
t3.MYI
t3.frm

...
--------------------------------------------------------------------------
The servers were restarted 0 times
Spent 0.000 of 8 seconds executing testcases

Completed: Failed 1/1 tests, 0.00% were successful.

Failing test(s): main.mysqlhotcopy_myisam