Here is a list of some shortcomings of Zettelstore. They are planned to be solved.

• All zettel must be indexed to enable full query functionality; otherwise, some zettel may not be returned.
• Quoted attribute values are not yet supported in Zettelmarkup (e.g. {key="value with spaces"}).
• The horizontal tab character (U+0009) is not fully supported by the parser.
• Citation keys are not yet supported.
• Changes to the content syntax are not reflected in the file extension.
• File names containing additional text beyond the zettel identifier are not always preserved.
• Case sensitivity in file names is not consistently handled. Some file systems distinguish between upper and lower case (e.g., Linux, sometimes macOS), while others do not (e.g., default macOS, most Windows systems). Zettelstore cannot detect these differences. Avoid using files that differ only by case in your directory boxes or file boxes.
• …

Ideas about future development are documented in its own wiki page.

Planned changes are documented in a ticket report.