This is most likely happening because your project.json file for your project is larger than our file size limit of 5MB. The project.json is the file that contains data about your project, including all of the blocks.
Scratch 3.0 project.json files are larger than Scratch 2.0 project.json files. So if your project was last saved as a Scratch 2 project, loading it into Scratch 3 will make the same data take up more space. You won't be able to save in that condition, but your old data will still be readable.
In order to fix the problem, you must remove content from your project. One way you can do this is by using clones to copy sprites rather than duplicating sprites. You can also look to see if you have any unused blocks in your program, such as blocks that aren't connected to a stack of blocks.
Sorry if this causes any inconvenience.