There are two possible reasons for this.
First, you manually overrode the frame onto the document page by Cmd (Mac) or Ctrl (Windows) + Shift clicking on the frame to make it active before placing your text. When you do this you are disconnecting that frame from the master text frame thread and new frames that are needed will be added using your margin and columns guides and any master frames that might be on a page will be ignored and will still be in place and available behind the new text frames. You might not notice these master frames are still there until you accidentally put other text inside them or you try to change the master text frame on the master page in some way and the text frame on the document page does not reflect your edit.
Second, you accidentally (or maybe purposely) clicked the “place gun” loaded text cursor on a guide. When you click the place gun on a guide you are telling InDesign that you want to create a new frame that is aligned to that guide rather than use any frame that may also already exist and also align to the guide. When this happens, ID will, again, create needed new frames according to the margin and column guides on your page and ignore any master text frames.
By paying close attention to the appearance of the place gun cursor you can tell whether InDesign is going to use an existing empty frame or create a new one. If the cursor is surrounded by large parentheses the existing frame will be used. If it has a square corner like the upper left corner of a page, then a new frame will be drawn. When that frame is drawn it will extend vertically from the point at which you click to the bottom margin guide, and will fill the width of whatever column you happen to click in. When autflowing, subsequent threaded frames will fill the guides from top margin to bottom margin.
For best results when placing content into an existing empty frame you should click in the empty space in the interior of the frame, well away from any guides.