I had the same issue with elpa and bzr 2.6p

$ bzr branch http://bzr.savannah.gnu.org/r/emacs/elpa 
bzr: ERROR: exceptions.AssertionError: ('not present: %r', StaticTuple('', '', 'TREE_ROOT'))                                                                                                                                    

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 930, in exception_to_return_code
    return the_callable(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 1141, in run_bzr
    ret = run(*run_argv)
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 673, in run_argv_aliases
    return self.run(**all_cmd_args)
  File "/usr/lib/python2.7/dist-packages/bzrlib/commands.py", line 697, in run
    return self._operation.run_simple(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 136, in run_simple
    self.cleanups, self.func, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 166, in _do_with_cleanups
    result = func(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/builtins.py", line 1508, in run
    source_branch=br_from)
  File "/usr/lib/python2.7/dist-packages/bzrlib/bzrdir.py", line 367, in sprout
    create_tree_if_local=create_tree_if_local)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 132, in run
    self.cleanups, self.func, self, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/cleanup.py", line 166, in _do_with_cleanups
    result = func(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/bzrdir.py", line 435, in _sprout
    hardlink=hardlink, from_branch=result_branch)
  File "/usr/lib/python2.7/dist-packages/bzrlib/bzrdir.py", line 907, in create_workingtree
    accelerator_tree=accelerator_tree, hardlink=hardlink)
  File "/usr/lib/python2.7/dist-packages/bzrlib/workingtree_4.py", line 1565, in initialize
    delta_from_tree=delta_from_tree)
  File "/usr/lib/python2.7/dist-packages/bzrlib/transform.py", line 2543, in build_tree
    delta_from_tree)
  File "/usr/lib/python2.7/dist-packages/bzrlib/transform.py", line 2659, in _build_tree
    precomputed_delta=precomputed_delta)
  File "/usr/lib/python2.7/dist-packages/bzrlib/transform.py", line 1747, in apply
    self._tree.apply_inventory_delta(inventory_delta)
  File "/usr/lib/python2.7/dist-packages/bzrlib/mutabletree.py", line 52, in tree_write_locked
    return unbound(self, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/bzrlib/workingtree_4.py", line 1320, in apply_inventory_delta
    state.update_by_delta(changes)
  File "/usr/lib/python2.7/dist-packages/bzrlib/dirstate.py", line 1387, in update_by_delta
    self._apply_insertions(insertions.values())
  File "/usr/lib/python2.7/dist-packages/bzrlib/dirstate.py", line 1439, in _apply_insertions
    path_utf8=path_utf8)
  File "/usr/lib/python2.7/dist-packages/bzrlib/dirstate.py", line 3116, in update_minimal
    raise AssertionError('not present: %r', entry_key)
AssertionError: ('not present: %r', StaticTuple('', '', 'TREE_ROOT'))

bzr 2.6b2 on python 2.7.3 (Linux-3.5.0-18-generic-x86_64-with-
    Ubuntu-12.10-quantal)
arguments: ['/usr/bin/bzr', 'branch',
    'http://bzr.savannah.gnu.org/r/emacs/elpa']
plugins: bash_completion[2.6b2], builddeb[2.7.0dev], changelog_merge[2.6b2],
    launchpad[2.6b2], netrc_credential_store[2.6b2], news_merge[2.6b2],
    po_merge[2.6b2], weave_fmt[2.6b2]
encoding: 'utf-8', fsenc: 'UTF-8', lang: 'en_US.UTF-8'

*** Bazaar has encountered an internal error.  This probably indicates a
    bug in Bazaar.  You can help us fix it by filing a bug report at
        https://bugs.launchpad.net/bzr/+filebug
    including this traceback and a description of the problem.

First attempt to clone the repo and bzr froze:

bzr branch http://bzr.savannah.gnu.org/r/emacs/elpa 
 17541kB    89kB/s | Fetching revisions:Inserting stream:Estimate 4305/10887                                                                                                                                                    
^Cbzr: interrupted