BUG: Some bug fixes and test changes

[carterbox]

Purpose

Squashes some bugs and modifies some tests in response to debugging some reconstruction comparisons with Junjing.

Approach

Pre-Merge Checklists

Submitter

• [ ] Write a helpfully descriptive pull request title.
• [ ] Organize changes into logically grouped commits with descriptive commit messages.
• [ ] Document all new functions.
• [ ] Click 'details' on the readthedocs check to view the updated docs.
• [ ] Write tests for new functions or explain why they are not needed.
• [ ] Address any complaints from pep8speaks.

Reviewer

• [ ] Actually read all of the code.
• [ ] Run the new code yourself; the included tests should make this easy.
• [ ] Write a summary of the changes as you understand them.
• [ ] Thank the submitter.