You will need to know a few things.
1.If the files you are using have coordinates systems assigned to them. I am unsure about shp files as i deal mainly in Mesh Datasets and Rasters. I do know that the CSV coordinates or Text file coordinates if they are GPS values ie:Lat Long have to be saved into a co-ordinates system value and that the QGIS project has to use the same coordinate system. The system uses the GPS coordinates to place the points accurately on the QGIS map. My Method is to use a site like bbox and use my Coordinates system of choice and record these Lat Long values into .CSV and then copy the same CRS settings from bbox within QGIS project then the shp and or imported files end up placed correctly when you load the imported text file layer or shp file. Also file formatting is important for text files like you have ie:CSV. If you set the CRS within the QGIS project if the layer you import in is from another CRS QGIS will automatically change this to the CRS you have set. If you do not have geographic information setout correctly you will have the problem you have now also another problem is if the file does not contain CRS information at all. But from what you are telling us this looks like a CRS mismatch problem.
2.What the coordinates system is for the files you have ie:epsg 4326 or 3857 these are two very different different systems that can drastically alter the placement of your points.
3.If they dont have a coordinate system assigned to them then you will need to assign one and use this same coordinates system within QGIS project before you import in the files. . 4.If the files do contain coordinate systems references then in QGIS you will need to set the project CRS system to the same as the files you have. This will apply the CRS to all layers you add to this project weather they are vectors, mesh, rasters and or base layers.
Good luck.