With a form I am saving the data to WordPress options, it's a big multidimensional array. The problem that I am facing is sometimes it misses a value in the array. I am not sure how to debug that as it works 80% of time. Can this be related as I am saving it as an array?
It depends, if you use the data, only as a whole. Lets say for configuration settings or something, then I would say, it's not a problem. But if you are doing queries on the data, like searching or fetching only 1 or 2 fields from that array.. you should use other solutions.
If you are missing some values from your array, are you sure these values are submitted from your form? (Are the fields not "disabled", or are these fields unchecked checkboxes?)