Answer: Although lack of pollination can cause baby squash to stop developing and rot, it sounds as though you have covered that possibility by hand pollinating. The other cause is a condition called blossom end rot. Squash blossom end rot happens due to a calcium deficiency. Calcium helps a plant create a stable structure. If a plant gets too little calcium while the fruit is developing, there is not enough to sufficiently build the cells on the fruit. In particular the bottom of the fruit, which grows the fastest, does not get enough calcium.
As the fruit gets larger, the cells begin to collapse, starting with those weakest cells at that bottom. At the location of the squash blossom, rot sets in and a black indentation appears.
To keep your squash from developing this problem, water evenly - If the plant goes through drastic changes in the amount of water it gets, it may not be able to take up the calcium it need at the crucial time when the fruit is being formed. Water evenly, not too much or too little.
If squash blossom end rot appears, remove the affected fruit and use a calcium rich foliar spray on the plant. This will ensue that the next round of squash that the plant grows will have sufficient calcium to grow correctly.
To address your concern about the majority of the blossoms being male rather than female, it's natural for a squash plant. As the plant matures it will begin to develop a larger ratio of female to male blossoms. You'll eventually have more squashes as the season progresses.
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