Somewhat redundant measures in California that are proposed at the same time generally are legally conflicting, which means that if both are passed, only the measure with the greatest margin actually goes into effect. I can't think of any real examples of simultaneous, partially-redundant measures that both had majority support and had no legal conflict, so that both went into effect, where you could make a plausible case that the kind of problem you describe was in play. Can you present any?
On further thought, the real issue is more related to the budget ones. E.g. there is technically no conflict between "don't raise taxes" and "spend money on X". Edited accordingly.
A bigger problem, in my opinion, is that a bare majority is sufficient to amend the state Constitution. I think at least a 60% supermajority should be required.
For instance, suppose the following: a majority of voters support Project A and a majority of voters support Project B, but Projects A and B are expensive and a majority of voters would oppose spending money on both Projects A and B.
If you do separate, parallel yes-or-no referendums on both A and B (as frequently happens in California), it is likely that both would pass, resulting in a sub-optimal outcome as a sub-majority wanted both.
With a smaller group of legislators, you can do things like non-binding votes to allow proponents to assess support and modify or withdraw their proposals accordingly (if A is more popular than B, then B can withdraw in favor of A) or sequential votes (if A has already passed, then people will vote no on B). The higher number of stakeholders involved with a referendum and the general cost of running an election make this less feasible with the direct democracy system.