Pixelmator Pro cannot import or edit vector files like EPS or AI formats. Users wanting to work with vectors in their photo editing workflow are blocked. Even online converters don't reliably solve this, forcing users to pre-rasterize vectors in other software.

Pixelmator Pro has minimal third-party plugin support compared to Photoshop's extensive library. Users relying on specialized plugins for retouching, effects, or workflow automation will find their options severely limited.

Unlike Photoshop and Affinity Photo, Pixelmator Pro cannot retain editable text when applying perspective or certain transformations. Text gets rasterized, forcing users to start over if edits are needed. This breaks standard design workflows for posters and thumbnails.

Users report a significant brush engine problem where brushes taper at the beginning of each stroke when pressure settings are applied. This makes illustration and digital painting work problematic, as strokes don't start naturally.

The feather/soft edge tool is not directly usable with objects. Users must create a mask first, and the mask approach is one-directional, adding extra steps to what should be a simple operation in professional editing.

There's no native way to add highlighted text to images without creating workarounds. Users making YouTube thumbnails, posters, and social media graphics find this basic feature frustratingly absent.

Pixelmator Pro does not support panorama stitching, a feature available in competitors like Affinity Photo and Photoshop. Photographers who shoot panoramas must use separate software to stitch images before editing.

While ML-powered subject selection exists, it's not always precise, especially on complex backgrounds or fine details like hair. Users report needing manual refinement more often than expected for an AI-powered tool.

A persistent bug causes warped objects to completely revert to their original rotation when warping is applied. This disrupts creative workflows and forces users to avoid certain editing combinations.

The iPad version has significant stability issues. Users report only a 50% chance of saving changes successfully, blank grey screens on launch, and a confusing UI with hidden menus requiring swipes and right-clicks to access features.

Following Apple's acquisition, Pixelmator Pro is now available through Apple Creator Studio subscription. Existing fans who appreciated the one-time purchase model are frustrated by subscription pushes, though standalone purchase still exists.

Despite the clean interface, some features are difficult to locate. The non-standard toolbar placement (layers on left instead of right) confuses users coming from Photoshop or Affinity Photo, extending the learning curve.