There are actually some good reasons. The default paste action will just paste text or HTML. However most OS clipboards have the ability to paste various types of content. If the clipboard contains a "better" media type it makes sense for the application to handle it and prevent the default action.

For example:

1. Pasting an image into a markdown field. A common action is to upload the image and insert the correct markup to embed it.

2. Pasting richer content inside an application. For example when copying a rich widget you may embed a text representation, HTML representation but if the user pastes the widget back into your app it is often best to keep a "native" representation that can be used to faithfully reconstruct the original data.