THis is just a guess,
Are you using tab controls? The references for the controls located on tab controls do not show up under Controls[].
If you want at those controls you have to determine which references are tab controls and then use the pages property to get at the control references of all of the controls on each page.
Nested tab controls require the same approach.
The only limit on controls/indicators I know of is 550.
(No! I did not write that code. I helped a customer dig themselves out).
Ben