I believe you're allowed to collect 100 eggs/24 hours but it doesn't reset at 12 AM Res time (which is when things like hatches reset). For example, if I picked up 50 eggs in the morning and 50 at night, the next day I would only be able to pick up 50 in the morning and 50 at night. Does that make any sense? xD
You can have as many eggs in your hatchery as you'd like (it can exceed 100). That doesn't factor in to the 100 egg/24 hrs you can pick up. This isn't a glitch and it usually doesn't become a problem anymore after you've played for longer. You develop your favorite creatu and also know which eggs are rarer and those become the only eggs you pick up. Since you only have about 3 hatches a day most people don't hit the 100 mark when picking up eggs because then they get old/spoil. Hope this clears things up!