The answer to your question how we differentiate your two cases is that they are framed in different contexts. The first is framed in the context of our theories of physics and the second in the context of probability theory. In each case, the context is the reason for the specified classification.
You offer these cases as sharing a similarity, that they are both anomalous. This is true of the first, but not of the second.
In the case of the first, we have to ask whether it is more likely that the account of the event is false or that the event is contrary to the laws of physics. If we are forced to accept the account of the event, we label it anomalous and look for an explanation. We may find one that is compatible with our existing theories, but cannot rule out in advance the more remote possibility that a successful explanation may involve altering existing theories. (Hence, anomalous events can be very useful in scientific research.)
Given your mention of miracles in the heading of the question, you may like to consider that the probability of a given event being caused by divine intervention will always be less likely than it being the result of something else – even if we do not yet know what that something is. Miracles have been very popular evidence of God’s existence (and power). So we have to acknowledge that someone who believes in divine intervention irrespective of the laws of nature will estimate the probabilities differently. Clearly, there is here no argument, either for or against the existence of God. You might like to consult Miracles (Stanford Encyclopedia of Philosophy)
What you have missed in your specification of the second case is that the outcome 200,000 consecutive heads is no more anomalous that 100,000 heads every time followed by 100,000 tails every time, or 200,000 heads and tails alternating or any other sequence. To put it another way, if you bet on the outcome of a single toss 200,000 times, the odds of success are always 1:2. If you bet on the outcome of two tosses at a time, no matter what sequence you bet on, there are 4 outcomes, so the odds are 1:4. If you bet on the outcome of three throws, the odds are 1:8. And so on.