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On some devices, the full bubbles (orange bubbles) or bubbles might not come up from the second world and onwards due to device running capacity, however when you collect the resources you should still get the fully generated resources.
One way to test the above is to leave your phone overnight (at least 6 hours). Get into the game the next day. If there are plants not showing the full bubbles or any bubbles, go to the Book section and find their info. The plant info page tells you the upper limit (capacity) of a plant. Go back to the main screen and tap the plant (please don't use the Techsaur feature), and take a notice of the number which comes up on the screen. It should be the same number as shown in the plant capacity section.
Please do let me know if the numbers are different. Please send over screenshots of the issue as well as your game ID (it's located in the game settings page.). Thank you!