Let me see if I can simplify this, from the perspective of someone with no formal scientific education.
Fred, using Newtonian physics, calculates the impact force of an apple striking the ground after falling from a tree. Jack measures various parameters of an actual apple, falling from an actual tree. He records the results from dozens of apples. Lisa compares Fred's math with Jack's measurements. The data sets match within acceptable margins of error. (For example, calibration factors within the measurement instrumentation; wind causing some of the apples to fall in a slightly different trajectory.)
Conclusion: The theory behind Newton's laws, for the purposes of apples falling from trees here on Earth, is demonstrated to be valid. For an alternate hypothesis/theory to be accepted, it must also be able to mathematically predict similar results for those same apples falling from those same trees. If the new hypothesis can not correctly make these predictions, then how can you trust it to be accurate about anything else?