TOC page numbers in Fixed Layout ePub not correct.

Are you working with the iPad Retina preset? At what resolution are you exporting the images? (Should be 72ppi if you use the iPad Retina preset, and 144ppi when using the regular (old) iPad preset.)

InDesign generates empty transparent PNG files if you have grouped empty frames lying around, for example. Those PNG files, while just consisting of transparent mono-coloured pixels, still wind up taking a LOT of memory while processing and rendering the result in a epub reader (or browser, etc.), because the raw uncompressed data is used and placed in video memory.

When InDesign generates these empty placeholder PNG files, and depending on the output resolution, very large (even huge) images are generated, which might cause memory issues during Epub export.

The only way to prevent InDesign from generating these utterly useless resource-gobbling empty PNG files is to fill the offending empty containers with your own tiny empty shim image, and tell InDesign to use that particular image file instead of generating its own files.

Here is the shim I use (it's invisible and 10x10px, but it is there! click to open and save the file):

What I do is place this in the frames which generate these empty PNG files, then set the object export option to Use Existing Image for graphic Objects (you could use an object style for this too), and set the fitting to Content to Frame.

That's it. It prevents InDesign from creating its own un-optimized filler PNG files.

Even when InDesign exports without issues, I always use this method (or fix things in code after), because the last thing you want is these ridiculously large empty PNG files reducing the performance and load times of your fixed ebooks on the device (because while these files are quite small file size-wise, they still take up the full uncompressed amount of video memory to display!)

This gets much worse when ebook designers decide to export at 144ppi or higher when using the iPad Retina preset in InDesign: this is not necessary, because exporting the images at 72ppi with this iPad preset generates the correct resolution for these devices.

Anyhoo, I hope this will fix your issues. It can be difficult to identify the culprits when you can't export in the first place - a solution would be to split up your file in pages of 10, or so, and export those. Then inspect the contents of the epub file. Any image that is empty and only carries a number points at the DIV container used in the html code, which again points at the frame used in the InDesign file (each frame in InDesign is converted to a DIV html container).

But if that sounds too daunting, look for empty frames in your pages, and either delete those, or use the shim.png trick.