I don't know what's going on here, but I hope you can reproduce it and
tell me.  The dev.allocpsa.net repo is a PHP timekeeping system, and I
wanted a Darcs checkout that only tracked the CLI client-side files.

$ mkdir alloc-cli
$ cd alloc-cli
$ darcs init
$ darcs pull http://dev.allocpsa.net -ap ^CLI --dont-prompt-for-dependencies
Warning: Cannot remove non-empty file ./project/templates/projectProductSaleS.tpl
Warning: Cannot remove non-empty file ./sale/lib/productSaleTransaction.inc.php
Warning: Cannot remove non-empty file ./images/icon_orb_green.png
Warning: Cannot remove non-empty file ./images/icon_orb_green.xcf
Warning: Cannot remove non-empty file ./images/icon_orb_red.png
Warning: Cannot remove non-empty file ./images/icon_orb_red.xcf
Warning: Cannot remove non-empty file ./images/icon_orb_yellow.png
Warning: Cannot remove non-empty file ./images/icon_orb_yellow.xcf
Finished pulling and applying.
Exception thrown by an atexit registered action:
./INSTALL/cron_jobs.txt-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/tidy_script-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/style_regen.py-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/install.sh-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/import.php-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/fix_tpl_values.vim-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/dump_structure.sh-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/db_structure.sql-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/cron_jobs.txt-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/tidy_script-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/style_regen.py-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/install.sh-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/import.php-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/fix_tpl_values.vim-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/dump_structure.sh-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/db_structure.sql-0: removeLink: inappropriate type (Not a directory)
Exception thrown by an atexit registered action:
./INSTALL/cron_jobs.txt-0: removeLink: inappropriate type (Not a directory)

Sorry for the delay in looking at this. What OS and filesystem type was 
this running on? Might there have been any permissioning issues leading 
to darcs being unable to remove its temporary files?

I think I've seen somewhat similar issues on funny filesystems on 
Windows, for example.