The glass fragments can contaminate the liquid. If it matters, then the glass fragments need to be filtered out. In chemistry experiments it may not matter immediately and the glass might be removed in later purification steps (like distillation, filtration or similar).
For example, in medical use, injectable medicines from a glass vial must be filtered before use. There are special needles with integrated filters that can be attached to suck the liquid out with a syringe. Then the needle can be changed to an injection needle.
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