Your Intraday MIS position  may not get squared off on the same day if the scrip hits circuit limits. In such cases it automatically transforms into a Delivery or Normal position. 

In case of cash markets if you have a buy trade pending it will result in delivery of the shares.  If your have sell trade pending it will result in short delivery and result in auction of the position in addition to penalty and difference payment.  

In case of F & O markets the un-squared off positions will get carried forward to the next trading day.

In such cases, it becomes the client's responsibility to close the position. Tradejini holds the right to square off such positions later at its discretion, even without issuing a margin call, if the necessary balance isn't present in the Tradejini account.

Why are the purchased shares not visible in the holdings?