This also happens with yakkety amd64 :

Sep  1 13:04:31 ubuntu [CLOUDINIT] util.py[DEBUG]: Running command ['growpart', '--dry-run', '/dev/vda', '1'] with allowed return codes [0] (shell=False, capture=True)
Sep  1 13:04:31 ubuntu [CLOUDINIT] util.py[DEBUG]: Running command ['growpart', '/dev/vda', '1'] with allowed return codes [0] (shell=False, capture=True)
Sep  1 13:04:31 ubuntu [CLOUDINIT] util.py[WARNING]: Failed: growpart /dev/vda 1
Sep  1 13:04:31 ubuntu [CLOUDINIT] util.py[DEBUG]: Failed: growpart /dev/vda 1#012Traceback (most recent call last):#012  File "/usr/lib/python3/dist-packages/cloudinit/config/cc_growpart.py", line 109, in resize#012    util.subp(["growpart", diskdev, partnum])#012  File "/usr/lib/python3/dist-packages/cloudinit/util.py", line 1832, in subp#012    cmd=args)#012cloudinit.util.ProcessExecutionError: Unexpected error while running command.#012Command: ['growpart', '/dev/vda', '1']#012Exit code: 2#012Reason: -#012Stdout: 'FAILED: failed to resize\n'#012Stderr: "attempt to resize /dev/vda failed. sfdisk output below:\n| GPT PMBR size mismatch (4612095 != 41943039) will be corrected by w(rite).\n| Backup files:\n|         PMBR (offset     0, size   512): /tmp/growpart.yWKkY4/orig.save-vda-0x00000000.bak\n|   GPT Header (offset   512, size   512): /tmp/growpart.yWKkY4/orig.save-vda-0x00000200.bak\n|  GPT Entries (offset  1024, size 16384): /tmp/growpart.yWKkY4/orig.save-vda-0x00000400.bak\n| \n| Disk /dev/vda: 20 GiB, 21474836480 bytes, 41943040 sectors\n| Units: sectors of 1 * 512 = 512 bytes\n| Sector size (logical/physical): 512 bytes / 512 bytes\n| I/O size (minimum/optimal): 512 bytes / 512 bytes\n| Disklabel type: gpt\n| Disk identifier: 1262F37F-7675-41D2-829F-7AC253FAB611\n| \n| Old situation:\n| \n| Device      Start     End Sectors  Size Type\n| /dev/vda1  227328 4612062 4384735  2.1G Linux filesystem\n| /dev/vda14   2048   10239    8192    4M BIOS boot\n| /dev/vda15  10240  227327  217088  106M EFI System\n| \n| Partition table entries are not in disk order.\n| \n| >>> Script header accepted.\n| >>> Script header accepted.\n| >>> Script header accepted.\n| >>> Script header accepted.\n| >>> Script header accepted.\n| >>> Created a new GPT disklabel (GUID: 1262F37F-7675-41D2-829F-7AC253FAB611).\n| Created a new partition 1 of type 'Linux filesystem' and of size 19.9 GiB.\n| /dev/vda2: Created a new partition 14 of type 'BIOS boot' and of size 4 MiB.\n| /dev/vda15: Created a new partition 15 of type 'EFI System' and of size 106 MiB.\n| /dev/vda16: \n| New situation:\n| \n| Device      Start      End  Sectors  Size Type\n| /dev/vda1  227328 41943006 41715679 19.9G Linux filesystem\n| /dev/vda14   2048    10239     8192    4M BIOS boot\n| /dev/vda15  10240   227327   217088  106M EFI System\n| \n| Partition table entries are not in disk order.\n| \n| The partition table has been altered.\n| Calling ioctl() to re-read partition table.\n| Re-reading the partition table failed.: Device or resource busy\n| The kernel still uses the old table. The new table will be used at the next reboot or after you run partprobe(8) or kpartx(8).\n***** WARNING: Resize failed, attempting to revert ******\n512+0 records in\n512+0 records out\n512 bytes copied, 0.000625739 s, 818 kB/s\n512+0 records in\n512+0 records out\n512 bytes copied, 0.000617735 s, 829 kB/s\n16384+0 records in\n16384+0 records out\n16384 bytes (16 kB, 16 KiB) copied, 0.0828234 s, 198 kB/s\n***** Appears to have gone OK ****\n"
Sep  1 13:04:31 ubuntu [CLOUDINIT] util.py[DEBUG]: resize_devices took 0.213 seconds