The reason this is happening is because the `slds-table` class is applying a padding to the `td` elements within the lightning input date selector.

The exact style definition of this is

    .slds-table td,.slds-table th{
        padding:.25rem .5rem;
        white-space:nowrap;
        position:relative
    }

This style was never meant to be applied to the date picker which results in the cells within being too large to fit in the container.

This is the style that should be applied but is being overridden:

    .slds-datepicker td{
        padding:.25rem;
        text-align:center;
        font-size:.75rem
     }

This has other impacts that you didn't point out. For instance, when you mouse over the date picker, the rows of the inner table are highlighted grey which is also not supposed to happen.

The fix would be to stop using the class and apply your styles manually.