If a flower is not pollinated enough (it requires several visits), it can result in small or deformed squashes (such as small squashes with tapered ends, and only a few of the seeds inside maturing); hand pollination will help new flowers along (squash has male and female flowers). Sometimes cool weather will slow pollinators, causing inadequate pollination at the time of flower formation.
Since the fruit seem to be tasty and not misshapen, and if the plants seem healthy, it probably is not a virus, which can deform fruit as well.
Check the end of the fruit--if it is brown, it might be blossom-end rot, which is caused by not enough calcium intake. In this disorder, fruit develop up to a point, then brown at one end and rot. Even if soil has calcium, the plant needs enough water to draw it in--if you think this may be the cause, make sure the plants are consistently watered (but not waterlogged); check the soil pH to make sure it is not too acidic (below 5.5; optimum for growing, 6.0 to 6.5). Avoid too much nitrogen.
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