What are the cons of taking frequent breaks between intense exercise?

Usually when I begin a new form of exercise, usually done at home, I take frequent breaks (at most 3 mins each) to catch a breath. Although, I know it is important to keep the heart rate up. Even though it takes that much longer, I still end up completing the exercise. I usually exercise before I go to bed and drink A LOT OF WATER. Is this habit before getting used to the exercise really detrimental?
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What are the cons of taking frequent breaks between intense exercise?
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