If all data tokens in a sector's data slot have already been replaced by markers, and a player would mark another signal in that sector (for example, due to a Scan action or card effect), the following applies:

• The player may still place their marker in the sector, even though there are no data tokens left to take.
• The player does not gain a data token for this marker, since there are no data tokens remaining.
• Placing this marker still counts toward winning the sector when it is completed.

This is supported by the following rule:

Sometimes you might have the opportunity to place more markers than a sector can hold. This is okay. You don't get data for the excess markers, but you can use them to help you win the sector once it's completed.

EXAMPLE: Everyone is tied with 2 markers, but orange wins the sector because orange marked it last. (Orange got no data for the last marker, but it was worth it to win the sector.)
(Page 13)

Summary:
If all data tokens are gone, you may still place a marker, but you do not gain data for it. The marker still counts for sector control.

Source: page 13.

Source: Core Rulebook (pp. 12, 13, 14, 17, 28)